Wiki - User contributions [en]

File:F5 small RNA update.pptx

2012-05-10T07:33:39Z

Burrough: uploaded a new version of "File:F5 small RNA update.pptx"

FANTOM5 analysis call

2012-05-10T07:32:35Z

Burrough: /* May 10th */

Weekly telephone calls open to all collaborators are held every '''Thursday 17:00 -18:00 JST'''. In case of Japanese holidays or special events, no call will be held. In such cases, information will be sent out to the FANTOM5 mailing list.

The agenda is decided by the FANTOM5 Management group at RIKEN. Suggestions can be sent to Piero Carninci. Agenda will be announced to the FANTOM5 mailing list every Wednesday. Presentation materials will be available on this page before each meeting.

The meetings will be recorded and saved here for later reference.

Phone numbers:

From outside of Japan: +81-3-4333-4000

From anywhere in Japan: 050-3786-6666 (in Japanese) or 0570-03-4444 (in English)

From the Tokyo Area: 03-4333-4444 (in Japanese) or 03-4333-4000 (in English)

From the Osaka Area: 06-7637-2222

You will be asked to enter conference ID followed by # and guest password followed by # to join the conference. Please find them below:

Conference id: 24711

Guest password: 3502

You will also be asked to state your name and press the # key.

[http://www.clearconference.jp/guide/download/clearconference_sheet_guest_e.pdf Call In Instructions for guest users (English)]

[http://www.clearconference.jp/guide/download/clearconference_sheet_guest.pdf Call In Instructions for guest users (Japanese)]

=May 10th=

Chair: Alistair Forrest

'''AGENDA'''

1. Progress report for this week by RIKEN OSC (Al Forrest)

2. MARA update (Michiel De Hoon, OSC) [[File:teleconference-20120510.pptx]]

3. Short RNAs update (Max Burroughs, OSC) [[File:F5_small_RNA_update.pptx‎]]

'''Audio File'''
The audio file from the call on April 19th (uploaded after the call): [[File:120510_F5_Telecon.zip]]

=May 3rd=

'''CANCELLED'''

Due to a [http://en.wikipedia.org/wiki/Constitution_Memorial_Day national holiday] in Japan, FANTOM5 Analysis Call will not be held.

=April 26th=

Chair: Piero Carninci

'''AGENDA'''

1. Progress report for this week by RIKEN OSC (Alistair FORREST) [[File:F5_Teleconference_april26.ppt]]

'''Audio File'''
The audio file from the call on April 19th (uploaded after the call): [[File:120426_F5_Telecon.zip]]

=April 19th=

Chair: Piero Carninci

'''AGENDA'''

1. Progress report for this week by RIKEN OSC

2. Presentation by Tom Freeman, Roslin Institute [https://fantom5-collaboration.gsc.riken.jp/webdav/home/freeman/ Presentation materials]

3. A brief presentation by Kenneth Baillie, Roslin Institute [http://www.altitude.org/fantom5 Presentation materials] (user name and password are the same as for the FANTOM5 Wiki page)

'''Audio File'''
The audio file from the call on April 19th (uploaded after the call): [[File:120419_F5_Telecon.zip]]

=April 12th=

Chair: Piero Carninci

'''AGENDA'''

1. Progress report for this week by RIKEN OSC
* Al - [[Satellite_submission]]
* Kawaji - [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/LRtest/120412-inter-intra-peak.pdf TSS usage inter/intra CAGE peaks]

'''Audio File'''
The audio file from the call on April 12th (uploaded after the call): [[File:120412_F5_Telecon.zip]]

=April 5th=

Chair: Piero Carninci

'''AGENDA'''

1. Progress report for this week by RIKEN OSC(Hideya KAWAJI and Alistair FORREST) [[File:120405-f5-telecon-kawaji.pdf]]

2. F5 core promoters(Albin SANDELIN, University of Copenhagen) [[File:F5_core_promoters_sandelin.pdf]]

'''Audio File'''
The audio file from the call on April 5th (uploaded after the call): [[File:120405_F5_Telecon.zip]]

=March 29th=

'''CANCELLED'''

Chair: Piero Carninci

'''AGENDA'''

1. Progress reports for this week by RIKEN OSC

2.

'''Audio File'''
The audio file from the call on March 29th (uploaded after the call): [[File:120329_F5_Telecon.zip]]

=March 22nd=

Chair: Piero Carninci

'''AGENDA'''

1. Progress reports for this week by RIKEN OSC

2. Presentation by Boris Lenhard and Vanja Haberle (Imperial College London/University of Bergen): "Distribution and enrichment of TF motifs and ChIPseq binding sites in cell-type specific promoters from ENCODE cell lines". [[Media:Distribution_of_TF_binding_sites_ENCODE_cell_lines.pdf]]

3. Presentation by Ryota Mori from Asai-Lab: "Analyzing the secondary structures of human lncRNAome". [[Media:LncRNA_2ndarystructure_080322.pdf]]

'''Audio File'''
The audio file from the call on March 22nd (uploaded after the call): [[File:120322_F5_Telecon.zip]]

=March 15th=

Chair: Piero Carninci

'''AGENDA'''

1. Progress reports for this week by RIKEN OSC

2. Presentation by group of Albin Sandelin, University of Copenhagen

'''Audio File'''
The audio file from the call on March 15th (uploaded after the call): [[File:120315_F5_Telecon.zip]]

=March 8th=

Chair: Piero Carninci

'''AGENDA'''

1. Progress reports for this week by RIKEN OSC(Timo Lassmann)

2. gencode10 lncRNA set by Andrea Tanzer (CRG) [[Media:atanzer_lncRNA_gen10_120308.pdf | lncRNA classification in gen10]]

'''Audio File'''
The audio file from the call on March 1st (uploaded after the call): [[File:120308_F5_Telecon.zip]]

3. Motif discussion points - Continued analysis from Michael and Christian's effect of background and length (minor interpretation from Al).
[[Media:Length_and_background_effects.pdf]]

=March 1st=

Chair: Piero Carninci

'''AGENDA'''

1. Progress reports for this week
Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_UPDATE_March1_2012.xls]]

2. Brief Presentation on RNA analysis by Cedric Notredame [[Media:RNAmapping_01032012.ppt]]

3. Motif discussion points
- Link to Michael's comparative analysis - effect of background and length.
https://fantom5-collaboration.gsc.riken.jp/webdav/home/rehli/ab%20initio%20motifs.pptx

- Motif finding vs Motif scoring - target vs background discussion

- CpG island promoters - tissue specificity in the CpG or the flanking sequences?

'''Audio File'''
The audio file from the call on March 1st (uploaded after the call): [[File:120301_F5_Telecon.zip]]

=February 23rd=

Chair: Piero Carninci

'''AGENDA'''

1. Progress reports for this week
Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_UPDATE_Feb23_2012.xls]]

'''Audio File'''
The audio file from the call on February 23rd (uploaded after the call): [[File:120223_F5_Telecon.zip]]

=February 16th=

Chair: Piero Carninci

'''AGENDA'''

1. Progress reports for this week

2. Discussion on motifs

3. Discussion on publication timeline ,

Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_UPDATE_Feb16_2012.xls]]
Publication timeline [[Media:Deadlines_Feb15_2012_for_distribution.xls]]

'''Audio File'''
The audio file from the call on February 16th (uploaded after the call): [[File:120216_F5_Telecon.zip]]

=February 9th=

Chair: Piero Carninci

'''AGENDA'''
* "Updates", RIKEN OSC, Japan
Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_Feb09_2012.xls]]

'''Audio File'''
The audio file from the call on February 9th (uploaded after the call): [[File:120209_F5_Telecon.zip]]

=February 2nd=

Chair: Piero Carninci

'''AGENDA'''
* "Using SUPERFAMILY to track evolutionary milestones in the FANTOM data.", Owen Rackham, University of Bristol, UK. Presentation files: [[File:F5evol.pdf]]
* "Updates", RIKEN OSC, Japan

'''Audio File'''
The audio file from the call on February 2nd (uploaded after the call): [[File:120202_F5_Telecon.zip]]

=January 26th=

Chair: Piero Carninci

'''AGENDA'''
* "Analysis update", RIKEN Omics Science Center. Presentation files will be uploaded here before the call
Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_Jan26_2012.xls]]

'''Audio File'''
The audio file from the call on January 12th (uploaded after the call): [[File:120126_F5_Telecon.zip]]

=January 19th=

Chair: Piero Carninci

'''AGENDA'''
* "Analysis update", RIKEN Omics Science Center. Presentation files will be uploaded here before the call

'''Audio File'''
The audio file from the call on January 12th (uploaded after the call): [[File:120119_F5_Telecon.zip]]

=January 12th=

Chair: Alistair Forrest

'''AGENDA'''
* "Analysis update", Hideya Kawaji, RIKEN Omics Science Center. Presentation files: [[File:120112-telecon-kawaji.pdf‎]]

'''Audio File'''
The audio file from the call on January 12th (uploaded after the call): [[File:120112_F5_Telecon.zip]]

=January 5th=

Analysis call CANCELED!

Next call will be held on January 12th

=December 22nd=

Chair: Piero Carninci

'''AGENDA'''
* "Pervasive divergent transcription identifies enhancers", Robin Andersson, University of Copenhagen, Denmark. PPT: [[File:Andersson_F5_telecon_dec_22_2011.ppt]], PDF: [[File:Andersson_F5_telecon_dec_22_2011.pdf]]
* "Analysis update", RIKEN Omics Science Center

'''Audio File'''
The audio file from the call on December 22nd (uploaded after the call): [[File:111222_F5_Telecon.zip]]

=December 15th=

Chair: Piero Carninci

'''AGENDA'''
* "Time course quality control", Erik Arner, RIKEN Omics Science Center, Japan. Presentation file will be uploaded here before the call
[[File:Timecourse_qc_20111215.pptx]]
[[File:Timecourse_qc_20111215.pdf‎]]
* "Analysis update", RIKEN Omics Science Center

'''Audio File'''
The audio file from the call on December 15th (uploaded after the call): [[File:111215_F5_Telecon.zip]]

=December 8th=

Chair: Piero Carninci

'''AGENDA'''
* "lncRNAome and lncRNA main paper update", Leonard Lipovich, Wayne State University, USA [[File:F5_Lipovich_08dec2011AnalysisCall.ppt]] [[File:F5_Lipovich_08dec2011AnalysisCall.pdf]]
* Update on promoterome paper", RIKEN OSC, Japan [[File:111208-telecon-kawaji.pdf‎]]
* [[Sample_QC]]

'''Audio File'''
The audio file from the call on December 8th (uploaded after the call): [[File:111208_F5_Telecon.zip]]

=December 1st=

Chair: Alistair Forrest

'''AGENDA'''
* "Status report on the ongoing analysis", Hideya kawaji, RIKEN OSC, Japan. [[File:111131-F5telecon-kawaji.pdf]]

'''Audio File'''
The audio file from the call on December 1st: [[File:111201_F5_Telecon.zip]]

=November 24th=

Chair: Piero Carninci

'''AGENDA'''
* "Status report on the ongoing analysis", RIKEN OSC, Japan. Presentation file will be uploaded before the call [[File:111124-f5-telecon-kawaji.pdf]]
* [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Sample_QC Sample QC] page by Al 

'''Audio File'''
Audio file from the call on November 24th (will be uploaded after the call): [[File:111124_F5_Telecon.zip]]

=November 17th=

Chair: Alistair Forrest

'''AGENDA'''
* "Brief Status report on the Promoterome paper", Alistair Forrest, RIKEN OSC, Japan. Promoterome update from Al [[Media:Promoterome_update_Nov17.doc]]

'''Audio File'''
Audio file from the call on November 17th: [[File:111117_F5_Telecon.zip]]

=November 10th=

Chair: Piero Carninci

'''AGENDA'''
* "Update on main paper analysis ", Promoterome update from Al [[File:Promoterome_update_Nov10.doc]]

* "Data analysis using the Fantom Sample Ontology", Chris Mungall, Lawrence Berkeley National Laboratory, USA. Presentation file: [[File:Fantom5-ontology.pptx]]

'''Audio File'''
Audio file from the call on November 10th will be uploaded here after the call [[File:111110_F5_Telecon.zip]]

=November 3rd=

On Thursday November 3rd, no FANTOM5 Analysis Call will be held since this day is a Japanese Holiday.

=October 27th=

Chair: Piero Carninci

'''AGENDA'''
* "Update on main paper analysis ", Hideya Kawaji, RIKEN OSC, Japan. Presentation file will be uploaded here before the call [[File:111027-telecon-kawaji.pdf‎ ]]

'''Audio File'''
Audio file from the call on October 27th: [[File:111027_F5_Telecon.zip]]

= October 13th =

The Analysis Call on October 13th has been cancelled. We are looking forward to meeting many of you here for the Koyo meeting!

=October 7th=

Chair: Piero Carninci

'''AGENDA'''
* "Homo sapiens complex motif collection (HoCoMoCo) and homotypic clusters of transcription factor binding sites", Ivan Kulakovskiy, Russian Academy of Sciences, Vavilov Institute of General Genetics, Russia. [[File:HOCOMOCO_and_homotypic_clusters_Kulakovskiy_et_al.pdf]]
* "Using MARA for analyzing time-courses" Piotr Balwierz , Universität Basel, Biozentrum, Switzerland.[[File:Mara-timecourses-balwierz.pdf]]

'''Audio File'''
Audio file from the call on September 29nd:[[File:111007_F5_Telecon.zip]]

=September 29nd=

Chair: Piero Carninci

'''AGENDA'''
* "Motif activity calculations on Update 11", Michiel de Hoon, RIKEN OSC, Japan. [[File:MARA_Michiel_20110929.pdf]]
* "Motif analysis of Fantom5 data: First insights" Vladimir Bajic, KAUST CBRC, Saubia Arabia. [[File:Teleconference_Sep_29_2011_Vlad.pdf]]

'''Audio File'''
Audio file from the call on September 29nd: [[File:110929_F5_Telecon.zip]].

=September 22nd=

Chair: Carsten Daub

'''AGENDA'''
* "TSS Classification", Timo Lassmann, RIKEN OSC, Japan and Sebastian Schmeier, KAUST CBRC, Saubia Arabia. Presentation file will be uploaded before the meeting [[file:TSSprediction_Sep22.pdf]] [[file:20110922_schmeier.pdf]]
* "De novo motif analysis of FANTOM5 CAGE-data" Michael Rehli, University Hospital Regensburg, Germany. Presentation: [[file:Rehli_Motifs2.pdf]]

'''Audio File'''
Audio file from the call on September 22nd: [[File:110922_F5_Telecon.zip]]

=September 15th=

Chair: Piero Carninci

'''AGENDA'''
* "Time-course sample kick-off: data availability, strategy, next steps", Carsten O. Daub, RIKEN OSC, Japan. Presentation [[file:FANTOM5_TC_-_Time_course_kick-off.pdf]]
* "NcRNAs in F5 time-courses: examples, resource, proposal" (5 minutes), Leonard Lipovich, Wayne State Univ., USA. [[file:F5_Lipovich_15sep2011AnalysisCall_mini.ppt]] [[file:F5_Lipovich_15sep2011AnalysisCall_mini.pdf]]

'''Audio File'''
Audio file from the call on September 15th: [[File:110915_F5_Telecon.zip]]

=September 8th=

Chair: Piero Carninci

'''AGENDA'''
* "The mammalian promoterome - paper punchlines", Alistair Forrest, RIKEN OSC, Japan. [[file:FANTOM5_TC_–_September_8th.ppt‎]]

'''Audio File'''
Audio file from the call on September 8th: [[File:110908_F5_Telecon.zip]]

=September 1st=

Chair: Piero Carninci

'''AGENDA'''
* "Status Update ", Hideya Kawaji, RIKEN OSC, Japan. [[file:110901-telecon-kawaji.pdf‎]]
* "Proposal for CAGE cluster annotation", Hideya Kawaji, RIKEN OSC, Japan. [[file:110901-cluster-annotation.pdf]]

'''Audio File'''
Audio file from the call on September 1st: [[File:110901_F5_Telecon.zip]]

=August 18th=

Chair: Piero Carninci

'''AGENDA'''

* "Exploring promoter type switching in developmental time courses", Boris Lenhard, University of Bergen, Norway. Presentation in PDF format: [[file:Lenhard_Analysis_Call_20110818.pdf]] . Please let me know (boris.lenhard@bio.uib.no) if you need the original Keynote file.

'''Audio File'''
Audio file from the call on August 18th 2011: [[File:110818_F5_Telecon.zip]].

=August 11th=

Chair: Piero Carninci

'''AGENDA'''

* "Status Update", Alistair Forrest, RIKEN OSC
* "F5 lncRNAome integration with hCAGE: inferring function and networks", Leonard Lipovich, Wayne State University, Detroit, USA
___(PPT: [[Media:F5_Lipovich_11aug2011AnalysisCall.ppt]], PDF: [[Media:F5_Lipovich_11aug2011AnalysisCall.pdf]])

'''Audio File'''
Audio file from the call on August 11th 2011: [[File:110811_F5_Telecon.zip]]‎

=August 4th=

Chair: Piero Carninci

'''AGENDA'''

* "Promoterome paper - plan, observations, requests for analysis ", Alistair Forrest, RIKEN OSC (presentation file - https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/File:AL_TC_AUG04.ppt)

'''Audio File'''
Audio file from the call on August 4th 2011: [[File:110804_F5_Telecon.zip]]

=July 28th=

Chair: Piero Carninci

'''AGENDA'''

* "CAGE clusters for the main paper", Hideya Kawaji, RIKEN OSC (presentation file - [[File:110728-F5-telecon-kawaji.pdf]])

'''Audio File'''
Audio file from the call on July 28th 2011: [[File:110728_F5_Telecon.zip]]

File:F5 small RNA update.pptx

2012-05-10T07:31:58Z

Burrough:

File:RNAseq HiSeq orders as of Oct2011 libID.xlsx

2012-03-26T04:44:22Z

Burrough: uploaded a new version of "File:RNAseq HiSeq orders as of Oct2011 libID.xlsx"

list of all RNAseq libraries and accompanying metadata, sequencing library ID included.

File:RNAseq HiSeq orders as of Oct2011 libID.xlsx

2012-03-22T05:06:47Z

Burrough: uploaded a new version of "File:RNAseq HiSeq orders as of Oct2011 libID.xlsx"

list of all RNAseq libraries and accompanying metadata, sequencing library ID included.

Noncoding RNA central page

2012-03-22T04:41:28Z

Burrough: /* RNA-seq */

Welcome to the central noncoding RNA page. This page serves as a repository for links to data of potential interest to computational collaborators, processed data hopefully of interest to wet-bench collaborators, and FANTOM5 paper pages centered on ncRNA analysis.

=ZENBU configuration=
This [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=bFijo7RhLRqlynp6K8LaSB;loc=hg19::chr7:41712147..41840341 link] leads to a ZENBU configuration containing tracks with pooled hCAGE, pooled short RNA, and pooled FANTOM5 RNA-seq expression data (edit: 11/9/2001--added CAGE-scan clusters, see F5 mailing list message 01096). Transcript structure is also provided in pooled CAGE-scan and RNA-seq tracks.

A couple of warnings:
# CAGE-scan/RNA-seq transcripts could crash your browser at loci with a large amount of expression.
# there are serious issues with short RNA expression values rooted in improper normalization.

We are aware of both of these issues; for issue #1 we are experimenting with new ways to view transcript structure and for issue #2 we are working on re-mapping and re-normalization of the short RNA data.

 
December 11th update

The latest [[Media:F5_human_lncRNAome_no_intra_redundancy_Nov19_n19599.bed|F5 human lncRNAome BED file (n=19599)]] is now available.
The corresponding [[Media:F5_human_lncRNAome(Jia%26Lipovich_Gencode_Lander).xls|F5 human lncRNAome Excel file]], which contains LEGENDS and ANNOTATIONS that cannot be incorporated into the BED, will be updated soon.
#As annotation (remember to select "bed_region" to obtain the full trancsript like complete structure)
#As a single track in DEX (somewhat more convenient that selecting it as an "annotation")
#Under this [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=-x3yFYR2FddrBGtv_AXvSC;loc=hg19::chr7:41712154..41840330 link], the latest lncRNAome dataset now replaces the previous ("F5_human_lncRNAome_28July2011") one.
#In addition the (latest as of November 11th) complete F5 human sample pooled expression ("Helicos all CTSS pooled human update Oct-25-2011 1409 samples") along with the updated F5 human lncRNAome is accessible thru the following [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=FxdzaeEqH9OgQSFaU3yZID link] 
To circumvent the issue pertaining to CAGE-scan potentially crashing your browser at loci with a large amount of expression, I recommend solely looking at the CAGEscan cluster track displaying the data as transcript like structures (the expression track not being particularly more informative than helicos CAGE data when expression levels are of interest). 

 
December 9th update

Complementing this wiki page, a ZENBU collaboration has been set up which should greatly facilitate the management of annotations while the lncRNAome core datasource is in the process of being refined. The zenbu collabiorartion is opned to anyone.
 https://fantom5-collaboration.gsc.riken.jp/zenbu/user/#section=collaborations 
Kindly drop me (nbertin@gsc.riken.jp) an email upon requesting to join, so that i can validate it (zenbu automated email notification system is still under development)

=FANTOM5 paper pages=
* long non-coding RNA main [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Long_noncoding_RNA_main_paper paper] is FANTOM5's definitive catalog and genomewide functional analysis of the human lncRNAome. Chains/networks of lncRNAs and coding RNAs will also be included.
* FANTOM5 novel lncRNA search with [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq RNA-seq] (this will be used to compile the nonredundant lncRNA gene and transcript catalog for the main paper above, but details are likely to give rise to separate papers)
* small RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Small_RNA_paper_page paper] (some of this will be included in lncRNA paper but there is likely enough here to stand on its own as a separate paper)

=Data for computational researchers=

==long noncoding RNA (lncRNA)==
* FANTOM5 gene-centric lncRNAome (Lipovich lab): [[Media:F5_human_lncRNAome_no_intra_redundancy_Nov19_n19599.bed]] (updated to reflect Cabili et al 2011 paper and Gencode)
* FANTOM5 sense/antisense pairing (Nicolas/Lipovich lab): [[Media:F5_human_sense-antisense_pairs_hg19.zip‎]] (update on S-AS co-expression from Nicolas coming soon)
* chains! [[File:F5_H_JIA_Nov2011_Engstrom_chainome_TU_hg19_all.zip]]
* novel predicted lncRNA from FANTOM5 hCAGE+RNAseq data (forthcoming)
* integrated Lipovich lncRNAome + novel lncRNA from FANTOM5 data (forthcoming)
* genes-and-transcripts (transcript-centric but with all transcripts assigned to genes) lncRNAome (in progress)

==small RNA==
* link to raw data (forthcoming, target: Nov. 15)
* miRNA expression table with normalization factors (forthcoming, target: Nov. 15)

==RNA-seq==
This also includes coding RNA, of course!
* link to currently-available raw data, ~18 libraries in twin samples of whole blood, CD19+, CD8+ (forthcoming)
* Cufflinks-assembled transcripts for the same ~18 libraries (forthcoming, target: Nov. 15)
* link to list of tissues and accompanying metadata selected for RNA-seq [[File:RNAseq_HiSeq_orders_as_of_Oct2011_libID.xlsx‎‎]]
* link to ~50 RNA-seq libraries raw data (~end of January)
* link to Cufflinks-assembled transcripts for the ~50 libraries (~mid-February)
* additional public data processed for our benefit! (soon, suggestions for good datasets to poach (ha! Alistair word!) are welcome)

== [[CAGEscan]] ==

[[Category:CAGEscan]]

* CAGEscan clusters in Zenbu:
**https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=xp3_LmYBDh9un3TLKQ7TT;loc=hg19::chr13:49225429..49287197

* links to currently-available raw data (69 samples):
** https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_013/f5pipeline/human.tissue.CAGEScan/00_human.tissue.CAGEScan.hg19.assay_sdrf.txt
** https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_013/f5pipeline/human.primary_cell.CAGEScan/00_human.primary_cell.CAGEScan.hg19.assay_sdrf.txt
** https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_013/f5pipeline/human.cell_line.CAGEScan/00_human.cell_line.CAGEScan.hg19.assay_sdrf.txt
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/Rat_cagescan/FASTQ/

* links to expression tables

=Processed data of potential interest to wet-bench collaborators=
As we don't have the initial processing of the data completed, these aren't quite ready yet. But we will update! Suggestions are more than welcome. We plan to make these available as excel/tab-delimited files with library name and ncRNA identifier (lncRNA, miRNA locus name, etc.) to look up in ZENBU.

==lncRNA-related==
* tissue-specific lncRNAs of potential interest
* lncRNAs displaying differential expression during a timecourse

==small RNA==
* primary cell-specific novel small RNA expression
* differential miRNA expression
* novel miRNAs of interest/tissue specific
* differential promoter RNA expression

Main Page

2012-03-22T04:39:58Z

Burrough: /* Collected samples, sample annotations, and data production status */

== What's new ==
* Phase 1 Freeze configurations are available for pooled samples. See [[ZENBU_Config]] page.
* [https://fantom5-collaboration.gsc.riken.jp/ucsc UCSC Genome Browser mirror] is continuously updated. New major functions become available - "track search" to find dataset with keywords, and "track hubs" to load external data (now Roadmap Epigenomic data can be shown via this function) (21st Sep, 2011)
* [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_013/ UPDATE_013] is released. See [[File_release]] (21st Sep, 2011)
* [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FANTOM5v5/ FANTOM5 ontology v5] covering all the update12 samples is provided by Terry Meehan (8th Sep, 2011)
* [https://fantom5-collaboration.gsc.riken.jp/resource_wiki/ Resource Wiki] is opened (Aug 5th, 2011)
* The same snapshot of UCSC database files has been [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/ucsc_database/ copied] (find "2011-06-20" directory under each genome assembly) (19th July, 2011)
* [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/110120-gene_expression_table-WP4/UPDATE_012/ gene expression files on UPDATE_012] are available (11th July, 2011)
* gene/promoter coordinates of the UCSC/ENCODE snapshot (20th June, 2011) has been [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/annotation_for_pipeline/ prepared] (6th July, 2011)
* [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_012/ UPDATE_012] is released. See [[File_release]] (4th July, 2011)
* Recent snapshot of UCSC/ENCODE (20th June, 2011) has been taken in [https://fantom5-collaboration.gsc.riken.jp/ucsc/cgi-bin/hgGateway UCSC RIKEN mirror] (4th July, 2011)
* Clusters uploaded ( Last update: June 1, 2011) [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=9bdAT9KFLx9sWuBetwwctC sample config]
*[https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_011/ UPDATE_011] with [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/110120-gene_expression_table-WP4/UPDATE_011/ gene expression]
*[[Data availability]]
* Wiki is up! [March 17, 2011]
*[[News archives]]

== FANTOM5 - five dimensions of cellular identity ==
Welcome to the FANTOM5 collaborator website. In FANTOM5 we are expanding the efforts made in FANTOM3 and 4 and aim to generate both a map of the majority of human promoters and comparative models of transcriptional regulatory network models of each cellular state. To achieve this we are carrying out deepCAGE sequencing on the Heliscope true single molecule sequencer on RNA isolated from every major human organ, over 200 cancer cell lines, 30 time courses of cellular differentiation, mouse developmental time courses and over 200 primary cell types

For those new to the FANTOM collaboration, please take some time to read the introductory material [[FANTOM5_overview]].

== FANTOM5 Main papers ==
* [[Promoterome_paper]]
* [[Time-courses main paper]]
* [[Long noncoding RNA main paper]]

== FANTOM5 Satellite papers ==
[[Satellite papers]]

== The first FANTOM5 meeting in February 2011 ==
We are planning to have the first of two FANTOM5 meetings in February 2011(Feb 20-25th). All participants will have an opportunity to present and attendants will be asked to [https://fantom5-collaboration.gsc.riken.jp/abstract/abstract.jsp submit an abstract] by February 10. [[First_FANTOM5_meeting_in_February|More information]]

== Collected samples, sample annotations, and data production status ==

This summary of samples and data production will be updated monthly. It details which samples are completed, scheduled or not yet scheduled. Please look here before emailing about sample scheduling. Sample annotations are also included.

*[[Image:Helicos_data_production_schedule_March15_v2.xls]] - '''NEW'''
*[[Image:CAGEscan production schedule February 2011.xls]]
*[[NanoCAGE]]
*[[Image:Short RNA Production Aug11.xls]] - 336 libraries (mostly primary cells) with matching helicos CAGE data
*[[File:RNAseq_HiSeq_orders_as_of_Oct2011_libID.xlsx‎]]

 

*Working draft of cell ontology update [[Image:CELL ONTOLOGY FANTOM5 Feb2011.xls]]

== Data Analysis and Integration (WP5) ==
Please put your data analysis results into this section [[Data Analysis and Integration]].

===== Current sections =====
Mapping and QC / Clustering , peak calling / Expression normalization and differential expression (based on genes, peaks, or whatever) / Annotation of promoter , 'gene' expression / Motif activity / Conservation , orthologous mapping (variome, basins) / Main paper specific analysis

== Resources ==

=== Data files ===

All the data produced in the FANTOM5 collaboration will be shared by any of the FANTOM5 collaborators to encourage a wide range of analysis with following the FANTOM5 rules. Please note that all the data is confidential and don't share with other people before public release. Please read [[FANTOM5_overview]] for the project plan.

All the data is accessible from [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/ share directory], and [[Dataset_introduction]] and [[File_release]] would be helpful to understand the data contents and the situation of the release.

=== Genome Browser ===

The FANTOM5 data is visible on two genome browsers, ZENBU (developed in RIKEN OSC, this allow us to manipulate data in a flexible way) and a local mirror of the UCSC Genome Browser.

*ZENBU [https://fantom5-collaboration.gsc.riken.jp/zenbu/ Homepage]. See [[ZENBU_Config]] for all the pre-configured views. See also [[ZENBU_Howto]], [[ZENBU_wishlist]], and [[ZENBU_administration]].
*[[UCSC_Local_Mirror]]

=== Additional information ===
*[[FANTOM5_overview]]
*[[Dataset_introduction]]
*[[File_release]]
*[[:Category:Methods_and_Protocols]]
*[https://fantom5-collaboration.gsc.riken.jp/files/doc/samples Sample documentation]
*[[Platform evaluation project]]

== [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php?title=Special:RecentChanges&feed=rss [[Image:Feed-icon-14x14.png]]] RSS/Atom feed ==

An good alternative to checking the wiki pages regularly to keep up-to-date with additions and modifications to all the FANTOM5 wiki page is to subscribe to the RSS feed of the [[Special:RecentChanges|"Recent Change"]] special page by clicking on [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php?title=Special:RecentChanges&feed=rss [[Image:Feed-icon-14x14.png]]] or : 

#Go to [[Special:RecentChanges|"Recent Change"]] 
#The bottom right toolbox provide links to RSS or Atom feed
#Choose your favorite RSS/Atom reader and stay up-to-date with all the modifications to any page or page additons

== Contacts/Mailing lists ==

=== Open for all FANTOM5 members ===
* fantom5@gsc.riken.jp (all FANTOM5 members; in principle, here is the place for discussion)
** A list of all collaborators can be viewed from the bottom of this page: [[FANTOM5_overview]]
* fantom5-wp5@gsc.riken.jp (WP5 is data analysis/integration work package; see [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_overview#Work_packages Work packages]; the place for bioinformatics related details)
* fantom5-samples@gsc.riken.jp (the place for sample related discussion - mainly sample annotation at this moment)

Each mailing list can have a different administrator. To be added to a specific mailing list, please email to: ''list_you_want_to_be_added_to''-admin@gsc.riken.jp . The requests will be redirected to the person who's in charge of that mailing list administration.

Examples:

* fantom5-wp5@gsc [Data analysis] email to ''fantom5-wp5-admin@gsc.riken.jp''
* fantom5-samples@gsc email to ''fantom5-samples-admin@gsc.riken.jp'' (or, directly, to ''m.lizio@gsc.riken.jp'')

=== Related but limited to RIKEN members ===
* fantom5-secretariat@gsc.riken.jp (FANTOM5 secretariat)
* fantom5-wp4@gsc.riken.jp (data control work package, 4). Any questions about Wiki, File Servers, Genome Browser, etc.
* fantom5_enquiries@gsc.riken.jp ; for non-FANTOM5 member to contact us. http://fantom.gsc.riken.jp/5/

 

 

----

Note: you can create your own account on this wiki freely. See the corner of top-right. Alternatively, you can use 'oscf5', with the same password to access here.

File:RNAseq HiSeq orders as of Oct2011 libID.xlsx

2012-03-22T04:37:56Z

Burrough: list of all RNAseq libraries and accompanying metadata, sequencing library ID included.

list of all RNAseq libraries and accompanying metadata, sequencing library ID included.

Long noncoding RNA main paper

2012-02-17T02:13:33Z

Burrough: /* Paper objectives, leadership, and communication */

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see the Noncoding RNA central [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Noncoding_RNA_central_page#RNA-seq page]. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives, leadership, and communication=
This paper aims to capture, and functionally define, the complete breadth and diversity of the non-redundant set of long noncoding RNA (lncRNA) genes in the human genome, while leveraging the unique qualities of FANTOM5 (hCAGE, RNAseq, >1k human cell and tissue samples) to fully characterize the cell type specificity, timecourse responsiveness, regulatory network participation, and evolutionary impact of these genes. For the purpose of this paper, it is important to note that our definition of lncRNAs is broader than that used by others, and includes, in addition to lincRNAs (long intergenic ncRNAs), all bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE, RNAseq, and/or pre-F5 cDNA/EST support. In addition, this paper will use genome organization and context coupled with hCAGE-measured expression of coding genes to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

Paper coordinators:
# Max Burroughs, Nicolas Bertin - main OSC coordinators and contacts (burrough@gsc.riken.jp and nbertin@gsc.riken.jp)
# Leonard Lipovich - senior coordinator (llipovich@med.wayne.edu)
# Al / Piero / WP4 / WP6 - overall supervision and co-direction; procurement and organization of datasets and validations.

Communication: We will have specific lncRNA main paper TeleConference calls, currently beginning after the main F5 call finishes.

=Outline of the paper, including key tasks and their assignments=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Koyo meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks will end up as satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. We already updated the non-redundant gene-centric human lncRNA catalog ("the F5 lncRNAome") with RNAs from Cabili et al Genes & Dev 2011. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard, Hui) Generation of the definitive gene-centric non-redundant FANTOM5 lncRNAome: "the" human lncRNA catalog ([[Media:F5_human_lncRNAome(Jia%26Lipovich_Gencode_Lander).xls|XLS]], [[Media:F5_human_lncRNAome_no_intra_redundancy_Nov19_n19599.bed|BED]])
## (Leonard, Hui) Inclusion of latest lncRNAs from the Cabili et al and the Gencode lncRNA Derrien et al papers - done, links at line above
## (Leonard, Hui) FUNDAMENTAL CHARACTERIZATION OF THE LNCRNAOME, identifying and counting lncRNAs in each of the following categories:
### standalone spliced lncRNA (consistent with "lincRNA" definition)
### standalone single-exon lncRNA
### lncRNA in a gene pair
#### bidirectionally promoted lncRNA
#### lncRNA nested intronically inside another gene, in the same direction as that gene
#### sense-antisense lncRNA
##### exonic antisense overlap with another gene
##### intronic antisense overlap with another gene
## (Max, Leonard, OSC) increasing the non-redundant lncRNAome by incorporating novel transcripts identified through FANTOM5 hCAGE and RNA-seq data - still To Do
# (WP4, Nicolas, Max, Kawaji-san, Leonard, Al) IN PROGRESS: generation of the transcript-centric (but gene-anchored) lncRNAome that will incorporate all transcripts of all lncRNA genes from across all of our lncRNAome data subsets. This is a significant upgrade to our current gene-centric (one usually arbitrarily selected transcript per gene) lncRNAome. 11 DEC 2011
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks from UPDATE012 and UPDATE013 associating with lncRNAome from the final filtered and normalized clustering values (Question: Where is the final list of Clusters that we should use for this? - LL)
# (Lukasz, and Tom Freeman!) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and (Tom Freeman?) in different tissues (made available on the wiki to sample providers)
## (Tom Freeman) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz, Win Hide, and Emmanuel Dimont!) Time course expression (IMPORTANT NOTE: THIS SUBSECTION MAY NEED TO MOVE FROM THE LNCRNA MAIN PAPER TO THE TIMECOURSE MAIN PAPER, DUE TO F5 TIMECOURSE DATA RELEASE CONSTRANTS.)
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
## (Win, Emmanuel) lncRNAs that go from low to high (or from high to low) in any specific timecourse
## (Win, Emmanuel) complete SwitchEngine analysis of lncRNA expression in timecourses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles (Question: Lukasz, how is this different from Tom F's stuff? - LL)
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)
# (how about Vlad or Boris J here?) tissue-specific differential promoter usage in lncRNAs; comparison to coding differential promoter usage

==General functional classification of lncRNAs==
Here we define the subset of lncRNAs likely to be acting in "cis" based on their genomic proximity to their putative cis-target or co-regulated genes, and develop specific, network-level functional predictions for individual lncRNAs based on co-expression. We also attempt to identify all lncRNAs involved in "trans" regulation (i.e. regulation of genes that reside outside of the lncRNA-encoding locus), and lncRNAs which may function as precursors for small/er RNA biogenesis. While there is some overlap in the analyses, due to the fact that some RNAs are probably involved in more than one of these three functional modalities, they are treated in separate sections below.

===cis-acting lncRNAs===
Specific tasks:
# (Nicolas, Leonard) Preliminary classification of cis-acting lncRNAs
## (Nicolas) calculating (PCC) and ranking sense-antisense co-expression at all ~ 2,800 manually annotated lncRNA-mRNA sense-antisense ("SAS") pairs (from the [[Media:F5_human_sense-antisense_pairs_hg19.zip|4,511-pair F5 SASome provided by Leonard)]] in latest data updates (012 and 013)
## (Leonard) annotation of the above into a curated set representing top-ranking co-regulated and anti-regulated lncRNA-mRNA SASpairs; emphasis on pairs containing mRNAs that encode transcriptional regulators (will use DAVID, Panther to ID them)
## (Leonard) [[Media:F5_H_JIA_Nov2011_Engstrom_chainome_TU_hg19_all.zip|update of the FANTOM3 human "Chainome" (already obtained from Engstrom et al) to hg19]]; identification of all lncRNA-containing chains; addition of new lncRNA-containing chains from non-Engstrom sources (Emily) to update the F5 Chainome
# cis-acting lncRNA analysis (each analysis performed on both the lncRNA-containing SASome extracted by Nicolas and the lncRNA-containing chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes (QUESTION: What is "locally-connected?" Are you referring to genomic neighbors here, but to in-trans co-expression or ontology-based connections when this outline item re-appears in the section below on trans-acting lncRNAs? - LL)
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains including both co-expressed gene ontology and cell tree ontology (i.e. co-expression of mRNAs in-cis, and/or of specific ontological categories of mRNAs in-trans, across related cell lineages gives clue to function)
### co-expression patterns to search for include lncRNA chains where all members are expressed; and chains where lncRNA is expressed and mRNA is not, and vice/versa.
## (Michiel) MARA analysis to see influence of cis-acting lncRNAs on transcriptional network (see motif enrichment section below)
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains (QUESTION: What is this? Is it redundant with stuff elsewhere in the outline? - LL)
### similar to above, search for potential effects on expression of chains in presence/absence of small RNA and its orientation
### (Eivind, Helena, Max, Martin, Asai-sensei / CBRC (see structure section below)) lncRNAs serving as possible small RNA precursors, and identification of novel structures in long RNAs

===trans-acting lncRNAs===
# (all) identification of potential trans-acting lncRNAs and their classes (classes: general trans-acting, Alu-element acting, and short RNA precursor transcripts)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
## (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results
## (Yulia) direct/inverse co-expression patterns of lncRNAs with known-gene mRNAs with Alu elements in 3'UTRs (based on Gong and Maquat 2011 Nature paper)
### (Hui, Leonard may assist w/ this) requires construction of the set of mRNAs with Alu elements in the 3' UTR to specifically look at effects of expression in these lncRNAs/potential target mRNAs
## (Sarah D.) identification of all lncRNAs that are cis-antisense to pseudogenes and that therefore may regulate in-trans the parental genes of the pseudogenes (check recent papers by Kevin Morris, this is a very "hot" area that we must cover)

===RNA processing of the F5 lncRNAome: empirical evidence from hCAGE/RNAseq/CAGEscan integration===
# RNA processing at exonic sense-antisense overlaps of lncRNA-mRNA pairs
## Cleavage and 5' capping of putative 3' cleavage fragments that map to SAS overlaps: capped (hCAGE and CAGEscan) data
### (Leonard) Case study: BDNF/BDNFOS (asymmetric capped cleavage products, symmetric uncapped short RNAs from SAS overlap)
### (?) Global analysis: Which of our ~ 2,800 annotated SAS overlaps give rise to capped? uncapped? symmetric? asymmetric? both?
# RNA processing of lncRNAs that serve as hosts of functional short RNAs
## Cleavage and 5' capping of 3' cleavage fragments located within the host lncRNA and after the mature short RNA sequence
### (Leonard) Case study: AK044422
# Human-mouse non-conservation of RNA processing: orthologous mouse loci that do not recapitulate the human pattern of capping and polarity (e.g. Bdnf); orthologous human loci that do not recapitulate the mouse pattern of cleave-and-cap after miRNA sequences (AK044422)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
## (Nicolas) Use CAGE-scan to look specifically for lncRNA TSSs inside repeats
## (Nicolas, Max) tabulation of all novel lncRNAs from this data and incorporation into non-redundant lncRNAome
# (Leonard, Hui) nonredundant incorporation of the combined data into the F5 lncRNAome: Go To Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset, task 1, subtask 3
# (Laurens) annotation of a set of novel lncRNAs (Question: Which set? Can Laurens annotate the novel RNAseq/CAGEscan hits, or was the original plan to rely on the HAVANA annotation of other F5 lncRNAome entries that was presented at the Koyo Meeting? - LL)

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Motif enrichment and lncRNA-specific regulatory programs
## Comparison 1: lncRNA promoters vs protein-coding-gene promoters (reported at Koyo Meeting)
## Comparison 2: promoters of cis-acting vs trans-acting lncRNAs (To Do)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome to identify possible candidates important to the transcriptional network

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse VS human for samples available in both species. Because lncRNAs are less conserved than protein-coding genes, it is possible that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken. There are three specific kinds of conservation that we are interested in analyzing: i) sequence (using UCSC TransMap and liftOver), ii) gene structure (location and presence/absence in the genome of lncRNAs; including chain conservation), iii) expression.

Specific tasks:
# (?) mapping human lncRNAs to mouse (TransMap/liftOver)
## (?) sequence conservation (-500/+500 TSS promoter regions vs. exons of full-length transcripts)
### (?) frequency
### (?) relative cis- vs. trans- conservation
### (?) promoter regions vs. full-length of transcripts
## (?) conservation of gene structure between the lncRNA genome location in human and the orthologous locus in mouse
### (?) presence/absence of lncRNAs (e.g. present in human, absent in mouse; but nearby known genes are conserved)
### (?) Positional Equivalents (Engstrom et al 2006 FANTOM3 definition)
#### (?) genomewide discovery of tag-only Positional Equivalents (human: cDNA/EST and hCAGE support; mouse: hCAGE-only support)
### (?) relative cis- vs. trans- conservation (QUESTION: How will we approach this? - LL)
### (?) conservation and partial conservation of the chainome
## (?) expression conservation
### (?) performed for conserved matches identified in 1.1 and also for conserved chains identified in 1.2
# (Yulia for global analysis, Leonard for annotation) frequency OF REPEAT-initiated TSS in lncRNA in humans vs. mouse (QUESTION: Do we have, or need, RNAseq/CAGEscan data from mouse for this? - LL)

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target cis-networks involving transcription of transcription factor or epigenetic modifier genes that are antisense to lncRNAs (in pairs or chains)
# (Max? Harukazu? WP6?) Which of these loci already have lncRNA-mRNA cis-co-expression (of a pair or of at least some part of a chain) in any of the cell line systems that are available for validation? What cell lines can we choose from?
# (coordinated by Harukazu, WP6) knockdown of lncRNAs, measuring local influence of lncRNAs to identify candidates for genome-wide perturbation experiments
## (WP6) probing transcriptional network perturbations through knockdown CAGE-seq
# (WP6) look into feasibility of overexpression experiments
## (Matthias Harbers) provide RIKEN / KK DNAFORM Clone IDs matching the lncRNAs that we may want to overexpress

==Structure features/subclassification of lncRNAs==
The intention here is to provide a classification of lncRNAs based on structural features (including computational secondary structure prediction and overlap with other genomic features) with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, recapping, positioning relative to other genome markers, etc.)

# (Eivind, Max, Helen) overlap with short RNA (TSS-based and other processing products), see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
# (?) overlap with other genome features
# (?) RNA-seq and splicing frequency
# (Hui Jia, Ben Brown) translational potential (small reading frames; overlap all exonic lncRNA sequences from the combined F5 lncRNAome -vs- public ENCODE proteogenomic data, and list all lncRNAs that are either mis-classified mRNAs or have evidence of ectopic translation)
# (CBRC) secondary structure of lncRNAs (NOTE: As only a small proportion of lncRNAs appear to be conserved, we are wondering what could be done to limit the influence of conservation on the secondary structure calculations. - LL, Max)
## small-RNA-like (pre-miRNA? piRNA-like? others?) structures (hairpins) and known-ncRNA like (tRNA-like?) structures (stems/loops) in all F5 cDNA/EST, RNAseq, and CAGEscan lncRNA sequences
### overlap of these predicted structures, if any, with known (UCSC sno/miRNA, tRNA etc tracks) small RNAs
## prediction of novel secondary structures specific to the long RNAs, including but not limited to pseudoknots; identification of novel structural lncRNAs that do not function by processing into shorter RNAs
## structure differences that correlate with our different lncRNA classifications (cis- vs trans-, chain vs. non-chain, convergent vs divergent structure in SASpairs, spliced lncRNAs vs. single-exon lncRNAs, known-shortRNA-containing vs non-containing, etc.)

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest, transcribed from enhancers (which act cryptically as lncRNA promoters) and involved in spatial and epigenetic cis-regulation of nearby and distant target genes. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

(BASIC QUESTION: Since eRNAs are polyA-, how do we look for them in F5 data? Which F5 datasets - hCAGE, RNAseq, CAGEscan, some subsets or all of these - retain polyA- transcripts? - LL)

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.) (HOW DO WE KNOW THIS FROM F5 DATA WHICH IS INHERENTLY NOT FULL-LENGTH? - LL, I think length distribution will also be dependent on overlap with RNA-seq, other statistics could include length between eRNA and nearest promoter, etc. - Max)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations
#(Leonard) curation of polyA+ cDNA/EST data suggesting polyA+ lncRNA transcription from loci that also give rise to polyA- eRNAs (e.g. EVF-2 locus DLX5/6 enhancer, and its paralogous locus DLX1/2 enhancer, clearly give rise to polyA+ lncRNAs in cDNA/EST data)

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
## How about specific identification of F5 lncRNAs in disease regions where no causative genes have yet been identified, and using these RNAs' expression profiles from F5 to make the case for their relevance to the particular disease/s? - LL
# (Leonard, Alka) Rett Syndrome and cis-chains
## clinical and translational relevance of the F5 lncRNAome: putative antisense eRNAs in a Rett region precisely recapitulate the exact brain expression profile of a leading Rett candidate gene
## Alka: inclusion of any info on patient deletions of this region depends on approval from and inclusion of your clinical collaborators - LL

==miRNA promoters: Please move this to Satellite page, or explain how it fits into the main paper :-) ==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) definition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses (Who-does-what and when; we will fold this into the outline above, as this is currently redundant)=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Small-scale (starting immediately):
** Current best targets from Emily and Leonard sent to the OSC (Max and Al) (done, 4 chains).
** Al and Max list of available experimental systems to Leonard (done for the 4 chains)
*** Leonard--> ZENBU curation of co-expression at these 4 loci in the available experimental systems (cell lines).
*** Max and Al--> discussion with WP6.
* Genome-wide (ongoing effort to get more cis-networks for validation):
** Hui/Leonard to update Par Engstrom's FANTOM3 chainome to hg19 [[Media:F5_H_JIA_Nov2011_Engstrom_chainome_TU_hg19_all.zip|- done!]]
** Nicolas to infer TF gene - lncRNA gene co-expression at TF-lncRNA SASpairs inside all updated FANTOM3 chains (To Do)
** Nicolas/Leonard to have ongoing pipeline of new chains to be validated by Al / WP6

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome (all done)
** Lukasz perform listed tasks (can begin ASAP; a "beta" run, do not wait for RNAseq)
*** listed tasks are performed again on classified cis-acting and trans-acting lncRNAs, looking for differences
* novel lncRNAs (from F5 RNAseq mapping to Al's new unique CAGE peaks) are added to the set
** potentially repeat above analyses a 3rd time (on all including F5-RNAseq-only lncRNAs)

==General functional classification of lncRNAs==
* Nicolas cis-acting classification (can begin now, don't wait for RNAseq; use F5 SASome and hg19-updated chainome)
** Leonard annotation of selected co-expressed lnc-mRNA cis-pairs, beginning with, but not limited to, TF-lncRNA pairs
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
** Leonard / Hui: basic identification of F5 lncRNAs that do, and don't, overlap any known small RNAs (miRNAs, snoRNAs, piwiRNAs)
*** identification of all lncRNAs that lack the potential to function as host of any known small RNAs
*** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two; re-do analysis (mid 2012 before submission) with new F5 RNAseq lncRNAs
* construction of the Alu element-containing mRNA list
** Yulia Alu elements role in trans-acting lncRNA gene-targeted expression

==Motif enrichment in promoter regions of lncRNAs (can begin now from 20k lncRNAome, don't wait for RNAseq)==
* Boris J. motif enrichment
* Michiel MARA

===Analysis of lncRNA promoters using ENCODE data===
* Finn : [[File:LncRNA_regulation_Rye_Drablos_23-11-2011.pdf]]

==lncRNA conservation in matching mouse primary cells==
* Al matched human/mouse samples
* Leonard assists in defining determinants of lncRNA conservation
** list of mouse/human sequence conserved sites
** ? sequence conservation
** ? genome structure conservation (includes chains)
*** expression conservation human/mouse based on conserved pairs identified in above two points
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
* ? compilation of conservation statistics (e.g. frequency, etc...)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* Eivind Max Helen overlap with short RNA see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
* CBRC general structural features of identified classes of lncRNAs
* take list of lncRNAs with overlapping short RNAs from above
** CBRC identification of "precursor" structure from RNA-seq and short RNA
** CBRC secondary structure predictions of lncRNAs in short RNA regions
*** CBRC integration of the two above
** CBRC identification of novel and nonconserved lncRNA structures (incl pseudoknots?) that do not depend on short RNA?

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation
* Leonard/Hui overlap of polyA- eRNAs with polyA+ lncRNAs; catalog of loci that give rise to both

==lncRNA and human disease overlap==
* global: Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* example: Leonard and Alka pursue Rett story
** potential eRNA and/or cis-regulatory lncRNA in FOXG1 region (partially done, presented at Koyo)

Long noncoding RNA main paper

2012-02-17T02:11:32Z

Burrough: /* Paper objectives, leadership, and communication */

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see the Noncoding RNA central [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Noncoding_RNA_central_page#RNA-seq page]. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives, leadership, and communication=
This paper aims to capture, and functionally define, the complete breadth and diversity of the non-redundant set of long noncoding RNA (lncRNA) genes in the human genome, while leveraging the unique qualities of FANTOM5 (hCAGE, RNAseq, >1k human cell and tissue samples) to fully characterize the cell type specificity, timecourse responsiveness, regulatory network participation, and evolutionary impact of these genes. For the purpose of this paper, it is important to note that our definition of lncRNAs is broader than that used by others, and includes, in addition to lincRNAs (long intergenic ncRNAs), all bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE, RNAseq, and/or pre-F5 cDNA/EST support. In addition, this paper will use genome organization and context coupled with hCAGE-measured expression of coding genes to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

Paper coordinators:
# Max Burroughs, Nicolas Bertin - main OSC contacts
# Leonard Lipovich - senior coordinator
# Al / Piero / WP4 / WP6 - overall supervision and co-direction; procurement and organization of datasets and validations.

Communication: We will have specific lncRNA main paper TeleConference calls, currently beginning after the main F5 call finishes.

=Outline of the paper, including key tasks and their assignments=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Koyo meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks will end up as satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. We already updated the non-redundant gene-centric human lncRNA catalog ("the F5 lncRNAome") with RNAs from Cabili et al Genes & Dev 2011. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard, Hui) Generation of the definitive gene-centric non-redundant FANTOM5 lncRNAome: "the" human lncRNA catalog ([[Media:F5_human_lncRNAome(Jia%26Lipovich_Gencode_Lander).xls|XLS]], [[Media:F5_human_lncRNAome_no_intra_redundancy_Nov19_n19599.bed|BED]])
## (Leonard, Hui) Inclusion of latest lncRNAs from the Cabili et al and the Gencode lncRNA Derrien et al papers - done, links at line above
## (Leonard, Hui) FUNDAMENTAL CHARACTERIZATION OF THE LNCRNAOME, identifying and counting lncRNAs in each of the following categories:
### standalone spliced lncRNA (consistent with "lincRNA" definition)
### standalone single-exon lncRNA
### lncRNA in a gene pair
#### bidirectionally promoted lncRNA
#### lncRNA nested intronically inside another gene, in the same direction as that gene
#### sense-antisense lncRNA
##### exonic antisense overlap with another gene
##### intronic antisense overlap with another gene
## (Max, Leonard, OSC) increasing the non-redundant lncRNAome by incorporating novel transcripts identified through FANTOM5 hCAGE and RNA-seq data - still To Do
# (WP4, Nicolas, Max, Kawaji-san, Leonard, Al) IN PROGRESS: generation of the transcript-centric (but gene-anchored) lncRNAome that will incorporate all transcripts of all lncRNA genes from across all of our lncRNAome data subsets. This is a significant upgrade to our current gene-centric (one usually arbitrarily selected transcript per gene) lncRNAome. 11 DEC 2011
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks from UPDATE012 and UPDATE013 associating with lncRNAome from the final filtered and normalized clustering values (Question: Where is the final list of Clusters that we should use for this? - LL)
# (Lukasz, and Tom Freeman!) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and (Tom Freeman?) in different tissues (made available on the wiki to sample providers)
## (Tom Freeman) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz, Win Hide, and Emmanuel Dimont!) Time course expression (IMPORTANT NOTE: THIS SUBSECTION MAY NEED TO MOVE FROM THE LNCRNA MAIN PAPER TO THE TIMECOURSE MAIN PAPER, DUE TO F5 TIMECOURSE DATA RELEASE CONSTRANTS.)
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
## (Win, Emmanuel) lncRNAs that go from low to high (or from high to low) in any specific timecourse
## (Win, Emmanuel) complete SwitchEngine analysis of lncRNA expression in timecourses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles (Question: Lukasz, how is this different from Tom F's stuff? - LL)
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)
# (how about Vlad or Boris J here?) tissue-specific differential promoter usage in lncRNAs; comparison to coding differential promoter usage

==General functional classification of lncRNAs==
Here we define the subset of lncRNAs likely to be acting in "cis" based on their genomic proximity to their putative cis-target or co-regulated genes, and develop specific, network-level functional predictions for individual lncRNAs based on co-expression. We also attempt to identify all lncRNAs involved in "trans" regulation (i.e. regulation of genes that reside outside of the lncRNA-encoding locus), and lncRNAs which may function as precursors for small/er RNA biogenesis. While there is some overlap in the analyses, due to the fact that some RNAs are probably involved in more than one of these three functional modalities, they are treated in separate sections below.

===cis-acting lncRNAs===
Specific tasks:
# (Nicolas, Leonard) Preliminary classification of cis-acting lncRNAs
## (Nicolas) calculating (PCC) and ranking sense-antisense co-expression at all ~ 2,800 manually annotated lncRNA-mRNA sense-antisense ("SAS") pairs (from the [[Media:F5_human_sense-antisense_pairs_hg19.zip|4,511-pair F5 SASome provided by Leonard)]] in latest data updates (012 and 013)
## (Leonard) annotation of the above into a curated set representing top-ranking co-regulated and anti-regulated lncRNA-mRNA SASpairs; emphasis on pairs containing mRNAs that encode transcriptional regulators (will use DAVID, Panther to ID them)
## (Leonard) [[Media:F5_H_JIA_Nov2011_Engstrom_chainome_TU_hg19_all.zip|update of the FANTOM3 human "Chainome" (already obtained from Engstrom et al) to hg19]]; identification of all lncRNA-containing chains; addition of new lncRNA-containing chains from non-Engstrom sources (Emily) to update the F5 Chainome
# cis-acting lncRNA analysis (each analysis performed on both the lncRNA-containing SASome extracted by Nicolas and the lncRNA-containing chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes (QUESTION: What is "locally-connected?" Are you referring to genomic neighbors here, but to in-trans co-expression or ontology-based connections when this outline item re-appears in the section below on trans-acting lncRNAs? - LL)
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains including both co-expressed gene ontology and cell tree ontology (i.e. co-expression of mRNAs in-cis, and/or of specific ontological categories of mRNAs in-trans, across related cell lineages gives clue to function)
### co-expression patterns to search for include lncRNA chains where all members are expressed; and chains where lncRNA is expressed and mRNA is not, and vice/versa.
## (Michiel) MARA analysis to see influence of cis-acting lncRNAs on transcriptional network (see motif enrichment section below)
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains (QUESTION: What is this? Is it redundant with stuff elsewhere in the outline? - LL)
### similar to above, search for potential effects on expression of chains in presence/absence of small RNA and its orientation
### (Eivind, Helena, Max, Martin, Asai-sensei / CBRC (see structure section below)) lncRNAs serving as possible small RNA precursors, and identification of novel structures in long RNAs

===trans-acting lncRNAs===
# (all) identification of potential trans-acting lncRNAs and their classes (classes: general trans-acting, Alu-element acting, and short RNA precursor transcripts)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
## (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results
## (Yulia) direct/inverse co-expression patterns of lncRNAs with known-gene mRNAs with Alu elements in 3'UTRs (based on Gong and Maquat 2011 Nature paper)
### (Hui, Leonard may assist w/ this) requires construction of the set of mRNAs with Alu elements in the 3' UTR to specifically look at effects of expression in these lncRNAs/potential target mRNAs
## (Sarah D.) identification of all lncRNAs that are cis-antisense to pseudogenes and that therefore may regulate in-trans the parental genes of the pseudogenes (check recent papers by Kevin Morris, this is a very "hot" area that we must cover)

===RNA processing of the F5 lncRNAome: empirical evidence from hCAGE/RNAseq/CAGEscan integration===
# RNA processing at exonic sense-antisense overlaps of lncRNA-mRNA pairs
## Cleavage and 5' capping of putative 3' cleavage fragments that map to SAS overlaps: capped (hCAGE and CAGEscan) data
### (Leonard) Case study: BDNF/BDNFOS (asymmetric capped cleavage products, symmetric uncapped short RNAs from SAS overlap)
### (?) Global analysis: Which of our ~ 2,800 annotated SAS overlaps give rise to capped? uncapped? symmetric? asymmetric? both?
# RNA processing of lncRNAs that serve as hosts of functional short RNAs
## Cleavage and 5' capping of 3' cleavage fragments located within the host lncRNA and after the mature short RNA sequence
### (Leonard) Case study: AK044422
# Human-mouse non-conservation of RNA processing: orthologous mouse loci that do not recapitulate the human pattern of capping and polarity (e.g. Bdnf); orthologous human loci that do not recapitulate the mouse pattern of cleave-and-cap after miRNA sequences (AK044422)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
## (Nicolas) Use CAGE-scan to look specifically for lncRNA TSSs inside repeats
## (Nicolas, Max) tabulation of all novel lncRNAs from this data and incorporation into non-redundant lncRNAome
# (Leonard, Hui) nonredundant incorporation of the combined data into the F5 lncRNAome: Go To Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset, task 1, subtask 3
# (Laurens) annotation of a set of novel lncRNAs (Question: Which set? Can Laurens annotate the novel RNAseq/CAGEscan hits, or was the original plan to rely on the HAVANA annotation of other F5 lncRNAome entries that was presented at the Koyo Meeting? - LL)

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Motif enrichment and lncRNA-specific regulatory programs
## Comparison 1: lncRNA promoters vs protein-coding-gene promoters (reported at Koyo Meeting)
## Comparison 2: promoters of cis-acting vs trans-acting lncRNAs (To Do)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome to identify possible candidates important to the transcriptional network

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse VS human for samples available in both species. Because lncRNAs are less conserved than protein-coding genes, it is possible that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken. There are three specific kinds of conservation that we are interested in analyzing: i) sequence (using UCSC TransMap and liftOver), ii) gene structure (location and presence/absence in the genome of lncRNAs; including chain conservation), iii) expression.

Specific tasks:
# (?) mapping human lncRNAs to mouse (TransMap/liftOver)
## (?) sequence conservation (-500/+500 TSS promoter regions vs. exons of full-length transcripts)
### (?) frequency
### (?) relative cis- vs. trans- conservation
### (?) promoter regions vs. full-length of transcripts
## (?) conservation of gene structure between the lncRNA genome location in human and the orthologous locus in mouse
### (?) presence/absence of lncRNAs (e.g. present in human, absent in mouse; but nearby known genes are conserved)
### (?) Positional Equivalents (Engstrom et al 2006 FANTOM3 definition)
#### (?) genomewide discovery of tag-only Positional Equivalents (human: cDNA/EST and hCAGE support; mouse: hCAGE-only support)
### (?) relative cis- vs. trans- conservation (QUESTION: How will we approach this? - LL)
### (?) conservation and partial conservation of the chainome
## (?) expression conservation
### (?) performed for conserved matches identified in 1.1 and also for conserved chains identified in 1.2
# (Yulia for global analysis, Leonard for annotation) frequency OF REPEAT-initiated TSS in lncRNA in humans vs. mouse (QUESTION: Do we have, or need, RNAseq/CAGEscan data from mouse for this? - LL)

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target cis-networks involving transcription of transcription factor or epigenetic modifier genes that are antisense to lncRNAs (in pairs or chains)
# (Max? Harukazu? WP6?) Which of these loci already have lncRNA-mRNA cis-co-expression (of a pair or of at least some part of a chain) in any of the cell line systems that are available for validation? What cell lines can we choose from?
# (coordinated by Harukazu, WP6) knockdown of lncRNAs, measuring local influence of lncRNAs to identify candidates for genome-wide perturbation experiments
## (WP6) probing transcriptional network perturbations through knockdown CAGE-seq
# (WP6) look into feasibility of overexpression experiments
## (Matthias Harbers) provide RIKEN / KK DNAFORM Clone IDs matching the lncRNAs that we may want to overexpress

==Structure features/subclassification of lncRNAs==
The intention here is to provide a classification of lncRNAs based on structural features (including computational secondary structure prediction and overlap with other genomic features) with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, recapping, positioning relative to other genome markers, etc.)

# (Eivind, Max, Helen) overlap with short RNA (TSS-based and other processing products), see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
# (?) overlap with other genome features
# (?) RNA-seq and splicing frequency
# (Hui Jia, Ben Brown) translational potential (small reading frames; overlap all exonic lncRNA sequences from the combined F5 lncRNAome -vs- public ENCODE proteogenomic data, and list all lncRNAs that are either mis-classified mRNAs or have evidence of ectopic translation)
# (CBRC) secondary structure of lncRNAs (NOTE: As only a small proportion of lncRNAs appear to be conserved, we are wondering what could be done to limit the influence of conservation on the secondary structure calculations. - LL, Max)
## small-RNA-like (pre-miRNA? piRNA-like? others?) structures (hairpins) and known-ncRNA like (tRNA-like?) structures (stems/loops) in all F5 cDNA/EST, RNAseq, and CAGEscan lncRNA sequences
### overlap of these predicted structures, if any, with known (UCSC sno/miRNA, tRNA etc tracks) small RNAs
## prediction of novel secondary structures specific to the long RNAs, including but not limited to pseudoknots; identification of novel structural lncRNAs that do not function by processing into shorter RNAs
## structure differences that correlate with our different lncRNA classifications (cis- vs trans-, chain vs. non-chain, convergent vs divergent structure in SASpairs, spliced lncRNAs vs. single-exon lncRNAs, known-shortRNA-containing vs non-containing, etc.)

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest, transcribed from enhancers (which act cryptically as lncRNA promoters) and involved in spatial and epigenetic cis-regulation of nearby and distant target genes. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

(BASIC QUESTION: Since eRNAs are polyA-, how do we look for them in F5 data? Which F5 datasets - hCAGE, RNAseq, CAGEscan, some subsets or all of these - retain polyA- transcripts? - LL)

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.) (HOW DO WE KNOW THIS FROM F5 DATA WHICH IS INHERENTLY NOT FULL-LENGTH? - LL, I think length distribution will also be dependent on overlap with RNA-seq, other statistics could include length between eRNA and nearest promoter, etc. - Max)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations
#(Leonard) curation of polyA+ cDNA/EST data suggesting polyA+ lncRNA transcription from loci that also give rise to polyA- eRNAs (e.g. EVF-2 locus DLX5/6 enhancer, and its paralogous locus DLX1/2 enhancer, clearly give rise to polyA+ lncRNAs in cDNA/EST data)

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
## How about specific identification of F5 lncRNAs in disease regions where no causative genes have yet been identified, and using these RNAs' expression profiles from F5 to make the case for their relevance to the particular disease/s? - LL
# (Leonard, Alka) Rett Syndrome and cis-chains
## clinical and translational relevance of the F5 lncRNAome: putative antisense eRNAs in a Rett region precisely recapitulate the exact brain expression profile of a leading Rett candidate gene
## Alka: inclusion of any info on patient deletions of this region depends on approval from and inclusion of your clinical collaborators - LL

==miRNA promoters: Please move this to Satellite page, or explain how it fits into the main paper :-) ==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) definition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses (Who-does-what and when; we will fold this into the outline above, as this is currently redundant)=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Small-scale (starting immediately):
** Current best targets from Emily and Leonard sent to the OSC (Max and Al) (done, 4 chains).
** Al and Max list of available experimental systems to Leonard (done for the 4 chains)
*** Leonard--> ZENBU curation of co-expression at these 4 loci in the available experimental systems (cell lines).
*** Max and Al--> discussion with WP6.
* Genome-wide (ongoing effort to get more cis-networks for validation):
** Hui/Leonard to update Par Engstrom's FANTOM3 chainome to hg19 [[Media:F5_H_JIA_Nov2011_Engstrom_chainome_TU_hg19_all.zip|- done!]]
** Nicolas to infer TF gene - lncRNA gene co-expression at TF-lncRNA SASpairs inside all updated FANTOM3 chains (To Do)
** Nicolas/Leonard to have ongoing pipeline of new chains to be validated by Al / WP6

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome (all done)
** Lukasz perform listed tasks (can begin ASAP; a "beta" run, do not wait for RNAseq)
*** listed tasks are performed again on classified cis-acting and trans-acting lncRNAs, looking for differences
* novel lncRNAs (from F5 RNAseq mapping to Al's new unique CAGE peaks) are added to the set
** potentially repeat above analyses a 3rd time (on all including F5-RNAseq-only lncRNAs)

==General functional classification of lncRNAs==
* Nicolas cis-acting classification (can begin now, don't wait for RNAseq; use F5 SASome and hg19-updated chainome)
** Leonard annotation of selected co-expressed lnc-mRNA cis-pairs, beginning with, but not limited to, TF-lncRNA pairs
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
** Leonard / Hui: basic identification of F5 lncRNAs that do, and don't, overlap any known small RNAs (miRNAs, snoRNAs, piwiRNAs)
*** identification of all lncRNAs that lack the potential to function as host of any known small RNAs
*** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two; re-do analysis (mid 2012 before submission) with new F5 RNAseq lncRNAs
* construction of the Alu element-containing mRNA list
** Yulia Alu elements role in trans-acting lncRNA gene-targeted expression

==Motif enrichment in promoter regions of lncRNAs (can begin now from 20k lncRNAome, don't wait for RNAseq)==
* Boris J. motif enrichment
* Michiel MARA

===Analysis of lncRNA promoters using ENCODE data===
* Finn : [[File:LncRNA_regulation_Rye_Drablos_23-11-2011.pdf]]

==lncRNA conservation in matching mouse primary cells==
* Al matched human/mouse samples
* Leonard assists in defining determinants of lncRNA conservation
** list of mouse/human sequence conserved sites
** ? sequence conservation
** ? genome structure conservation (includes chains)
*** expression conservation human/mouse based on conserved pairs identified in above two points
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
* ? compilation of conservation statistics (e.g. frequency, etc...)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* Eivind Max Helen overlap with short RNA see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
* CBRC general structural features of identified classes of lncRNAs
* take list of lncRNAs with overlapping short RNAs from above
** CBRC identification of "precursor" structure from RNA-seq and short RNA
** CBRC secondary structure predictions of lncRNAs in short RNA regions
*** CBRC integration of the two above
** CBRC identification of novel and nonconserved lncRNA structures (incl pseudoknots?) that do not depend on short RNA?

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation
* Leonard/Hui overlap of polyA- eRNAs with polyA+ lncRNAs; catalog of loci that give rise to both

==lncRNA and human disease overlap==
* global: Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* example: Leonard and Alka pursue Rett story
** potential eRNA and/or cis-regulatory lncRNA in FOXG1 region (partially done, presented at Koyo)

Small RNA data description

2011-11-09T09:16:15Z

Burrough:

=Introduction=
This page is intended to provide an overview of the current state of small RNA sequencing in the FANTOM5 project. It addresses the raw material and methods used in sequencing small RNA, methods used to map the sequences, data normalization strategies, and some quality control measures. For discussion on the F5 small RNA paper, please see this [ page]. For an overview of all noncoding RNA data and resources in FANTOM5, see this [ page].

=Sequencing Methods=
Small RNA for the FANTOM5 project was sequenced using the Illumina [http://www.illumina.com/truseq.ilmn TruSeq] kit, with 24 distinct samples multiplexed in a single Illumina HiSeq2000 lane. In each lane, a control (the standard mouse whole body, embryo E17.5 internal control used for all of FANTOM5) was sequenced with the same barcode.

=Source RNA=
To this point, small RNA sequencing has focused on the FANTOM5 panel of primary cells. Primary cell RNA was selected for small RNA-seq based on the following conditions: 1) availability of the sequences at the time the sequencing order was made and 2) preparation of the original RNA sample before delivery to RIKEN OSC did not exclude small RNAs.

The list of all sequenced samples is attached [ here]. As previously announced, additional time course samples will be selected for small RNA-seq and we will update the sample list when we get more information.

The following is a chart of the organism and F5 classification of all sequenced samples. While we have sequenced roughly ~360 samples, the number of replicates for each cell varies between 1-6 and the total number of distinct samples is 131.

--add chart here--

=Mapping=
Sequences were extracted and then mapped with the bwa alignment program (PMID: [ ]). The resulting bwa alignments were then used as "seeds" for alignment via the Delve short read alignment program developed by Timo Lassmann at RIKEN OSC. For more information see the following [ page]. Briefly, Delve assigns a probability representing the likelihood that an alignment is derived from a given location on the genome. For anyone preferring to use the original bwa alignments, these are provided in the final .bam alignment files as secondary mappings.

Links to the raw bam files for all libraries.

=Normalization=
take this from previous writings.

=Filtering=
Describe process.
List of all ids and samples.
List of all ids and samples to use in differential expression comparisons.

=Variance in Data=
Describe dispersion values in biological versus technical replicates.

Small RNA data description

2011-11-09T09:15:18Z

Burrough:

=Introduction=
This page is intended to provide an overview of the current state of small RNA sequencing in the FANTOM5 project. It addresses the raw material and methods used in sequencing small RNA, methods used to map the sequences, data normalization strategies, and some quality control measures. For discussion on the F5 small RNA paper, please see this [ page]. For an overview of all noncoding RNA data and resources in FANTOM5, see this [ page].

=Sequencing Methods=
Small RNA for the FANTOM5 project was sequenced using the Illumina [http://www.illumina.com/truseq.ilmn TruSeq] kit, with 24 distinct samples multiplexed in a single Illumina HiSeq2000 lane. In each lane, a control (the standard mouse whole body, embryo E17.5 internal control used for all of FANTOM5) was sequenced with the same barcode.

=Source RNA=
To this point, small RNA sequencing has focused on the FANTOM5 panel of primary cells. Primary cell RNA was selected for small RNA-seq based on the following conditions: 1) availability of the sequences at the time the sequencing order was made and 2) preparation of the original RNA sample before delivery to RIKEN OSC did not exclude small RNAs.

The list of all sequenced samples is attached [ here]. As previously announced, additional time course samples will be selected for small RNA-seq and we will update the sample list when we get more information.

The following is a chart of the organism and F5 classification of all sequenced samples. While we have sequenced roughly ~360 samples, the number of replicates for each cell varies between 1-6 and the total number of distinct samples is 131.

--add chart here--

=Mapping=
Sequences were extracted and then mapped with the bwa alignment program (PMID: [ ]). The resulting bwa alignments were then used as "seeds" for alignment via the Delve short read alignment program developed by Timo Lassmann at RIKEN OSC. For more information see the following [ page]. Briefly, Delve assigns a probability representing the likelihood that an alignment is derived from a given location on the genome. For anyone preferring to use the original bwa alignments, these are provided in the final .bam alignment files as secondary mappings.

Links to the raw bam files for all libraries.

=Normalization=
take this from previous writings.

=Variability in Data=
Describe dispersion values.

=Filtering=
Describe process.
List of all ids and samples.
List of all ids and samples to use in differential expression comparisons.

Small RNA data description

2011-11-09T09:10:05Z

Burrough:

Small RNA data description

2011-11-09T08:32:18Z

Burrough: Created page with '=Introduction= This page is intended to provide an overview of the current state of small RNA sequencing in the FANTOM5 project. It addresses the raw material and methods used in…'

Noncoding RNA central page

2011-11-09T08:05:39Z

Burrough: /* ZENBU configuration */

Noncoding RNA central page

2011-11-09T08:05:24Z

Burrough: /* ZENBU configuration */

Noncoding RNA central page

2011-11-09T08:04:00Z

Burrough: /* ZENBU configuration */

Long noncoding RNA main paper

2011-11-07T05:08:10Z

Burrough: /* Structure features/subclassification of lncRNAs */

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see the Noncoding RNA central [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Noncoding_RNA_central_page#RNA-seq page]. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives, leadership, and communication=
This paper aims to capture, and functionally define, the complete breadth and diversity of the non-redundant set of long noncoding RNA (lncRNA) genes in the human genome, while leveraging the unique qualities of FANTOM5 (hCAGE, RNAseq, >1k human cell and tissue samples) to fully characterize the cell type specificity, timecourse responsiveness, regulatory network participation, and evolutionary impact of these genes. For the purpose of this paper, it is important to note that our definition of lncRNAs is broader than that used by others, and includes, in addition to lincRNAs (long intergenic ncRNAs), all bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE, RNAseq, and/or pre-F5 cDNA/EST support. In addition, this paper will use genome organization and context coupled with hCAGE-measured expression of coding genes to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

Paper leadership:
# Max Burroughs, Nicolas Bertin - listed first authors; main OSC contacts
# Leonard Lipovich - listed last (principal) author; key coordinator
# Al / Piero / WP4 / WP6 - overall supervision and co-direction; procurement and organization of datasets and validations.

Communication: We will have specific lncRNA main paper TeleConference calls (times TBD). These are different from the main F5 TCs.

=Tasks for the paper=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Koyo meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks will end up as satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. We are currently updating the non-redundant gene-centric human lncRNA catalog ("the F5 lncRNAome") with RNAs from Cabili et al Genes & Dev 2011. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard, Hui) Generation of the definitive gene-centric non-redundant FANTOM5 lncRNAome: "the" human lncRNA catalog
## (Leonard, Hui) Inclusion of latest lncRNAs from the Cabili et al and the Gencode lncRNA Derrien et al papers - done
## (Leonard, Hui) FUNDAMENTAL CHARACTERIZATION OF THE LNCRNAOME, identifying and counting lncRNAs in each of the following categories:
### standalone spliced lncRNA (consistent with "lincRNA" definition)
### standalone single-exon lncRNA
### lncRNA in a gene pair
#### bidirectionally promoted lncRNA
#### lncRNA nested intronically inside another gene, in the same direction as that gene
#### sense-antisense lncRNA
##### exonic antisense overlap with anothe gene
##### intronic antisense overlap with another gene
## (Max, Leonard, OSC) increasing the non-redundant lncRNAome by incorporating novel transcripts identified through FANTOM5 hCAGE and RNA-seq data - still To Do
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks from UPDATE012 and UPDATE013 associating with lncRNAome from the final filtered and normalized clustering values (Question: Where is the final list of Clusters that we should use for this? - LL)
# (Lukasz, and Tom Freeman!) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and (Tom Freeman?) in different tissues (made available on the wiki to sample providers)
## (Tom Freeman) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz, Win Hide, and Emmanuel Dimont!) Time course expression
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
## (Win, Emmanuel) lncRNAs that go from low to high (or from high to low) in any specific timecourse
## (Win, Emmanuel) complete SwitchEngine analysis of lncRNA expression in timecourses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles (Question: Lukasz, how is this different from Tom F's stuff? - LL)
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)
# (how about Vlad or Boris J here?) tissue-specific differential promoter usage in lncRNAs; comparison to coding differential promoter usage

==General functional classification of lncRNAs==
Here we define the subset of lncRNAs likely to be acting in "cis" based on their genomic proximity to their putative cis-target or co-regulated genes, and develop specific, network-level functional predictions for individual lncRNAs based on co-expression. We also attempt to identify all lncRNAs involved in "trans" regulation (i.e. regulation of genes that reside outside of the lncRNA-encoding locus), and lncRNAs which may function as precursors for small/er RNA biogenesis. While there is some overlap in the analyses, due to the fact that some RNAs are probably involved in more than one of these three functional modalities, they are treated in separate sections below.

===cis-acting lncRNAs===
Specific tasks:
# (Nicolas, Leonard) Preliminary classification of cis-acting lncRNAs
## (Nicolas) calculating (PCC) and ranking sense-antisense co-expression at all ~ 2,800 manually annotated lncRNA-mRNA sense-antisense ("SAS") pairs (from the 4,511-pair F5 SASome provided by Leonard) in latest data updates (012 and 013)
## (Leonard) annotation of the above into a curated set representing top-ranking co-regulated and anti-regulated lncRNA-mRNA SASpairs; emphasis on pairs containing mRNAs that encode transcriptional regulators (will use DAVID, Panther to ID them)
## (Leonard) update of the FANTOM3 human "Chainome" (already obtained from Engstrom et al) to hg19; identification of all lncRNA-containing chains; addition of new lncRNA-containing chains from non-Engstrom sources (Emily) to update the F5 Chainome
# cis-acting lncRNA analysis (each analysis performed on both the lncRNA-containing SASome extracted by Nicolas and the lncRNA-containing chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes (QUESTION: What is "locally-connected?" Are you referring to genomic neighbors here, but to in-trans co-expression or ontology-based connections when this outline item re-appears in the section below on trans-acting lncRNAs? - LL)
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains including both co-expressed gene ontology and cell tree ontology (i.e. co-expression of mRNAs in-cis, and/or of specific ontological categories of mRNAs in-trans, across related cell lineages gives clue to function)
### co-expression patterns to search for include lncRNA chains where all members are expressed; and chains where lncRNA is expressed and mRNA is not, and vice/versa.
## (Michiel) MARA analysis to see influence of cis-acting lncRNAs on transcriptional network (see motif enrichment section below)
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains (QUESTION: What is this? Is it redundant with stuff elsewhere in the outline? - LL)
### similar to above, search for potential effects on expression of chains in presence/absence of small RNA and its orientation
### (Eivind, Helena, Max, Martin, Asai-sensei / CBRC (see structure section below)) lncRNAs serving as possible small RNA precursors, and identification of novel structures in long RNAs

===trans-acting lncRNAs===
# (all) identification of potential trans-acting lncRNAs and their classes (classes: general trans-acting, Alu-element acting, and short RNA precursor transcripts)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
## (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results
## (Yulia) direct/inverse co-expression patterns of lncRNAs with known-gene mRNAs with Alu elements in 3'UTRs (based on Gong and Maquat 2011 Nature paper)
### (Hui, Leonard may assist w/ this) requires construction of the set of mRNAs with Alu elements in the 3' UTR to specifically look at effects of expression in these lncRNAs/potential target mRNAs
## (?) identification of all lncRNAs that are cis-antisense to pseudogenes and that therefore may regulate in-trans the parental genes of the pseudogenes (check recent papers by Kevin Morris, this is a very "hot" area that we must cover)

===RNA processing of the F5 lncRNAome: empirical evidence from hCAGE/RNAseq/CAGEscan integration===
# RNA processing at exonic sense-antisense overlaps of lncRNA-mRNA pairs
## Cleavage and 5' capping of putative 3' cleavage fragments that map to SAS overlaps: capped (hCAGE and CAGEscan) data
### (Leonard) Case study: BDNF/BDNFOS (asymmetric capped cleavage products, symmetric uncapped short RNAs from SAS overlap)
### (?) Global analysis: Which of our ~ 2,800 annotated SAS overlaps give rise to capped? uncapped? symmetric? asymmetric? both?
# RNA processing of lncRNAs that serve as hosts of functional short RNAs
## Cleavage and 5' capping of 3' cleavage fragments located within the host lncRNA and after the mature short RNA sequence
### (Leonard) Case study: AK044422
# Human-mouse non-conservation of RNA processing: orthologous mouse loci that do not recapitulate the human pattern of capping and polarity (e.g. Bdnf); orthologous human loci that do not recapitulate the mouse pattern of cleave-and-cap after miRNA sequences (AK044422)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
## (Nicolas) Use CAGE-scan to look specifically for lncRNA TSSs inside repeats
## (Nicolas, Max) tabulation of all novel lncRNAs from this data and incorporation into non-redundant lncRNAome
# (Leonard, Hui) nonredundant incorporation of the combined data into the F5 lncRNAome: Go To Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset, task 1, subtask 3
# (Laurens) annotation of a set of novel lncRNAs (Question: Which set? Can Laurens annotate the novel RNAseq/CAGEscan hits, or was the original plan to rely on the HAVANA annotation of other F5 lncRNAome entries that was presented at the Koyo Meeting? - LL)

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Motif enrichment and lncRNA-specific regulatory programs
## Comparison 1: lncRNA promoters vs protein-coding-gene promoters (reported at Koyo Meeting)
## Comparison 2: promoters of cis-acting vs trans-acting lncRNAs (To Do)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome to identify possible candidates important to the transcriptional network

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse VS human for samples available in both species. Because lncRNAs are less conserved than protein-coding genes, it is possible that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken. There are three specific kinds of conservation that we are interested in analyzing: i) sequence (using UCSC TransMap and liftOver), ii) gene structure (location and presence/absence in the genome of lncRNAs; including chain conservation), iii) expression.

Specific tasks:
# (?) mapping human lncRNAs to mouse (TransMap/liftOver)
## (?) sequence conservation (-500/+500 TSS promoter regions vs. exons of full-length transcripts)
### (?) frequency
### (?) relative cis- vs. trans- conservation
### (?) promoter regions vs. full-length of transcripts
## (?) conservation of gene structure between the lncRNA genome location in human and the orthologous locus in mouse
### (?) presence/absence of lncRNAs (e.g. present in human, absent in mouse; but nearby known genes are conserved)
### (?) Positional Equivalents (Engstrom et al 2006 FANTOM3 definition)
#### (?) genomewide discovery of tag-only Positional Equivalents (human: cDNA/EST and hCAGE support; mouse: hCAGE-only support)
### (?) relative cis- vs. trans- conservation (QUESTION: How will we approach this? - LL)
### (?) conservation and partial conservation of the chainome
## (?) expression conservation
### (?) performed for conserved matches identified in 1.1 and also for conserved chains identified in 1.2
# (Yulia for global analysis, Leonard for annotation) frequency OF REPEAT-initiated TSS in lncRNA in humans vs. mouse (QUESTION: Do we have, or need, RNAseq/CAGEscan data from mouse for this? - LL)

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target cis-networks involving transcription of transcription factor or epigenetic modifier genes that are antisense to lncRNAs (in pairs or chains)
# (Max? Harukazu? WP6?) Which of these loci already have lncRNA-mRNA cis-co-expression (of a pair or of at least some part of a chain) in any of the cell line systems that are available for validation? What cell lines can we choose from?
# (coordinated by Harukazu, WP6) knockdown of lncRNAs, measuring local influence of lncRNAs to identify candidates for genome-wide perturbation experiments
## (WP6) probing transcriptional network perturbations through knockdown CAGE-seq
# (WP6) look into feasibility of overexpression experiments
## (Matthias Harbers) provide RIKEN / KK DNAFORM Clone IDs matching the lncRNAs that we may want to overexpress

==Structure features/subclassification of lncRNAs==
The intention here is to provide a classification of lncRNAs based on structural features (including computational secondary structure prediction and overlap with other genomic features) with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, recapping, positioning relative to other genome markers, etc.)

# (Eivind, Max, Helen) overlap with short RNA (TSS-based and other processing products), see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
# (?) overlap with other genome features
# (?) RNA-seq and splicing frequency
# (Hui Jia, Ben Brown) translational potential (small reading frames; overlap all exonic lncRNA sequences from the combined F5 lncRNAome -vs- public ENCODE proteogenomic data, and list all lncRNAs that are either mis-classified mRNAs or have evidence of ectopic translation)
# (CBRC) secondary structure of lncRNAs (NOTE: As only a small proportion of lncRNAs appear to be conserved, we are wondering what could be done to limit the influence of conservation on the secondary structure calculations. - LL, Max)
## small-RNA-like (pre-miRNA? piRNA-like? others?) structures (hairpins) and known-ncRNA like (tRNA-like?) structures (stems/loops) in all F5 cDNA/EST, RNAseq, and CAGEscan lncRNA sequences
### overlap of these predicted structures, if any, with known (UCSC sno/miRNA, tRNA etc tracks) small RNAs
## prediction of novel secondary structures specific to the long RNAs, including but not limited to pseudoknots; identification of novel structural lncRNAs that do not function by processing into shorter RNAs
## structure differences that correlate with our different lncRNA classifications (cis- vs trans-, chain vs. non-chain, convergent vs divergent structure in SASpairs, spliced lncRNAs vs. single-exon lncRNAs, known-shortRNA-containing vs non-containing, etc.)

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest, transcribed from enhancers (which act cryptically as lncRNA promoters) and involved in spatial and epigenetic cis-regulation of nearby and distant target genes. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

(BASIC QUESTION: Since eRNAs are polyA-, how do we look for them in F5 data? Which F5 datasets - hCAGE, RNAseq, CAGEscan, some subsets or all of these - retain polyA- transcripts? - LL)

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.) (HOW DO WE KNOW THIS FROM F5 DATA WHICH IS INHERENTLY NOT FULL-LENGTH? - LL, I think length distribution will also be dependent on overlap with RNA-seq, other statistics could include length between eRNA and nearest promoter, etc. - Max)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations
#(Leonard) curation of polyA+ cDNA/EST data suggesting polyA+ lncRNA transcription from loci that also give rise to polyA- eRNAs (e.g. EVF-2 locus DLX5/6 enhancer, and its paralogous locus DLX1/2 enhancer, clearly give rise to polyA+ lncRNAs in cDNA/EST data)

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
## How about specific identification of F5 lncRNAs in disease regions where no causative genes have yet been identified, and using these RNAs' expression profiles from F5 to make the case for their relevance to the particular disease/s? - LL
# (Leonard, Alka) Rett Syndrome and cis-chains
## clinical and translational relevance of the F5 lncRNAome: putative antisense eRNAs in a Rett region precisely recapitulate the exact brain expression profile of a leading Rett candidate gene
## Alka: inclusion of any info on patient deletions of this region depends on approval from and inclusion of your clinical collaborators - LL

==miRNA promoters: Please move this to Satellite page, or explain how it fits into the main paper :-) ==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) definition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Al and Max list of available experimental systems to Leonard
* Current best targets from Emily and Leonard sent to the OSC (Max and Al).
** Max and Al--> discussion with WP6.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome
** Lukasz perform listed tasks
*** listed tasks are performed again on classified cis-acting and trans-acting lncRNAs, looking for differences
* novel lncRNAs are added to the set
** potentially repeat above analyses

==General functional classification of lncRNAs==
* Nicolas cis-acting classification
** Leonard annotation of formal "Chainome"
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
** Leonard / Hui: basic identification of F5 lncRNAs that do, and don't, overlap any known small RNAs (miRNAs, snoRNAs, piwiRNAs)
*** identification of all lncRNAs that lack the potential to function as host of any known small RNAs
*** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two
* construction of the Alu element-containing mRNA list
** Yulia Alu elements role in trans-acting lncRNA gene-targeted expression

==Motif enrichment in promoter regions of lncRNAs==
* Boris motif enrichment
* Michiel MARA

==lncRNA conservation in matching mouse primary cells==
* Al matched human/mouse samples
* Leonard assists in defining determinants of lncRNA conservation
** list of mouse/human sequence conserved sites
** ? sequence conservation
** ? genome structure conservation (includes chains)
*** expression conservation human/mouse based on conserved pairs identified in above two points
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
* ? compilation of conservation statistics (e.g. frequency, etc...)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* Eivind Max Helen overlap with short RNA see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
* CRBC general structural features of identified classes of lncRNAs
* take list of lncRNAs with overlapping short RNAs from above
** CRBC identification of "precursor" structure from RNA-seq and short RNA
** CRBC secondary structure predictions of lncRNAs in short RNA regions
*** CRBC integration of the two above

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation

==lncRNA and human disease overlap==
* Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* Leonard and Alka pursue Rhett story

Long noncoding RNA main paper

2011-11-07T05:06:36Z

Burrough: /* eRNA analysis */

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see the Noncoding RNA central [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Noncoding_RNA_central_page#RNA-seq page]. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives, leadership, and communication=
This paper aims to capture, and functionally define, the complete breadth and diversity of the non-redundant set of long noncoding RNA (lncRNA) genes in the human genome, while leveraging the unique qualities of FANTOM5 (hCAGE, RNAseq, >1k human cell and tissue samples) to fully characterize the cell type specificity, timecourse responsiveness, regulatory network participation, and evolutionary impact of these genes. For the purpose of this paper, it is important to note that our definition of lncRNAs is broader than that used by others, and includes, in addition to lincRNAs (long intergenic ncRNAs), all bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE, RNAseq, and/or pre-F5 cDNA/EST support. In addition, this paper will use genome organization and context coupled with hCAGE-measured expression of coding genes to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

Paper leadership:
# Max Burroughs, Nicolas Bertin - listed first authors; main OSC contacts
# Leonard Lipovich - listed last (principal) author; key coordinator
# Al / Piero / WP4 / WP6 - overall supervision and co-direction; procurement and organization of datasets and validations.

Communication: We will have specific lncRNA main paper TeleConference calls (times TBD). These are different from the main F5 TCs.

=Tasks for the paper=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Koyo meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks will end up as satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. We are currently updating the non-redundant gene-centric human lncRNA catalog ("the F5 lncRNAome") with RNAs from Cabili et al Genes & Dev 2011. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard, Hui) Generation of the definitive gene-centric non-redundant FANTOM5 lncRNAome: "the" human lncRNA catalog
## (Leonard, Hui) Inclusion of latest lncRNAs from the Cabili et al and the Gencode lncRNA Derrien et al papers - done
## (Leonard, Hui) FUNDAMENTAL CHARACTERIZATION OF THE LNCRNAOME, identifying and counting lncRNAs in each of the following categories:
### standalone spliced lncRNA (consistent with "lincRNA" definition)
### standalone single-exon lncRNA
### lncRNA in a gene pair
#### bidirectionally promoted lncRNA
#### lncRNA nested intronically inside another gene, in the same direction as that gene
#### sense-antisense lncRNA
##### exonic antisense overlap with anothe gene
##### intronic antisense overlap with another gene
## (Max, Leonard, OSC) increasing the non-redundant lncRNAome by incorporating novel transcripts identified through FANTOM5 hCAGE and RNA-seq data - still To Do
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks from UPDATE012 and UPDATE013 associating with lncRNAome from the final filtered and normalized clustering values (Question: Where is the final list of Clusters that we should use for this? - LL)
# (Lukasz, and Tom Freeman!) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and (Tom Freeman?) in different tissues (made available on the wiki to sample providers)
## (Tom Freeman) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz, Win Hide, and Emmanuel Dimont!) Time course expression
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
## (Win, Emmanuel) lncRNAs that go from low to high (or from high to low) in any specific timecourse
## (Win, Emmanuel) complete SwitchEngine analysis of lncRNA expression in timecourses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles (Question: Lukasz, how is this different from Tom F's stuff? - LL)
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)
# (how about Vlad or Boris J here?) tissue-specific differential promoter usage in lncRNAs; comparison to coding differential promoter usage

==General functional classification of lncRNAs==
Here we define the subset of lncRNAs likely to be acting in "cis" based on their genomic proximity to their putative cis-target or co-regulated genes, and develop specific, network-level functional predictions for individual lncRNAs based on co-expression. We also attempt to identify all lncRNAs involved in "trans" regulation (i.e. regulation of genes that reside outside of the lncRNA-encoding locus), and lncRNAs which may function as precursors for small/er RNA biogenesis. While there is some overlap in the analyses, due to the fact that some RNAs are probably involved in more than one of these three functional modalities, they are treated in separate sections below.

===cis-acting lncRNAs===
Specific tasks:
# (Nicolas, Leonard) Preliminary classification of cis-acting lncRNAs
## (Nicolas) calculating (PCC) and ranking sense-antisense co-expression at all ~ 2,800 manually annotated lncRNA-mRNA sense-antisense ("SAS") pairs (from the 4,511-pair F5 SASome provided by Leonard) in latest data updates (012 and 013)
## (Leonard) annotation of the above into a curated set representing top-ranking co-regulated and anti-regulated lncRNA-mRNA SASpairs; emphasis on pairs containing mRNAs that encode transcriptional regulators (will use DAVID, Panther to ID them)
## (Leonard) update of the FANTOM3 human "Chainome" (already obtained from Engstrom et al) to hg19; identification of all lncRNA-containing chains; addition of new lncRNA-containing chains from non-Engstrom sources (Emily) to update the F5 Chainome
# cis-acting lncRNA analysis (each analysis performed on both the lncRNA-containing SASome extracted by Nicolas and the lncRNA-containing chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes (QUESTION: What is "locally-connected?" Are you referring to genomic neighbors here, but to in-trans co-expression or ontology-based connections when this outline item re-appears in the section below on trans-acting lncRNAs? - LL)
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains including both co-expressed gene ontology and cell tree ontology (i.e. co-expression of mRNAs in-cis, and/or of specific ontological categories of mRNAs in-trans, across related cell lineages gives clue to function)
### co-expression patterns to search for include lncRNA chains where all members are expressed; and chains where lncRNA is expressed and mRNA is not, and vice/versa.
## (Michiel) MARA analysis to see influence of cis-acting lncRNAs on transcriptional network (see motif enrichment section below)
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains (QUESTION: What is this? Is it redundant with stuff elsewhere in the outline? - LL)
### similar to above, search for potential effects on expression of chains in presence/absence of small RNA and its orientation
### (Eivind, Helena, Max, Martin, Asai-sensei / CBRC (see structure section below)) lncRNAs serving as possible small RNA precursors, and identification of novel structures in long RNAs

===trans-acting lncRNAs===
# (all) identification of potential trans-acting lncRNAs and their classes (classes: general trans-acting, Alu-element acting, and short RNA precursor transcripts)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
## (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results
## (Yulia) direct/inverse co-expression patterns of lncRNAs with known-gene mRNAs with Alu elements in 3'UTRs (based on Gong and Maquat 2011 Nature paper)
### (Hui, Leonard may assist w/ this) requires construction of the set of mRNAs with Alu elements in the 3' UTR to specifically look at effects of expression in these lncRNAs/potential target mRNAs
## (?) identification of all lncRNAs that are cis-antisense to pseudogenes and that therefore may regulate in-trans the parental genes of the pseudogenes (check recent papers by Kevin Morris, this is a very "hot" area that we must cover)

===RNA processing of the F5 lncRNAome: empirical evidence from hCAGE/RNAseq/CAGEscan integration===
# RNA processing at exonic sense-antisense overlaps of lncRNA-mRNA pairs
## Cleavage and 5' capping of putative 3' cleavage fragments that map to SAS overlaps: capped (hCAGE and CAGEscan) data
### (Leonard) Case study: BDNF/BDNFOS (asymmetric capped cleavage products, symmetric uncapped short RNAs from SAS overlap)
### (?) Global analysis: Which of our ~ 2,800 annotated SAS overlaps give rise to capped? uncapped? symmetric? asymmetric? both?
# RNA processing of lncRNAs that serve as hosts of functional short RNAs
## Cleavage and 5' capping of 3' cleavage fragments located within the host lncRNA and after the mature short RNA sequence
### (Leonard) Case study: AK044422
# Human-mouse non-conservation of RNA processing: orthologous mouse loci that do not recapitulate the human pattern of capping and polarity (e.g. Bdnf); orthologous human loci that do not recapitulate the mouse pattern of cleave-and-cap after miRNA sequences (AK044422)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
## (Nicolas) Use CAGE-scan to look specifically for lncRNA TSSs inside repeats
## (Nicolas, Max) tabulation of all novel lncRNAs from this data and incorporation into non-redundant lncRNAome
# (Leonard, Hui) nonredundant incorporation of the combined data into the F5 lncRNAome: Go To Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset, task 1, subtask 3
# (Laurens) annotation of a set of novel lncRNAs (Question: Which set? Can Laurens annotate the novel RNAseq/CAGEscan hits, or was the original plan to rely on the HAVANA annotation of other F5 lncRNAome entries that was presented at the Koyo Meeting? - LL)

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Motif enrichment and lncRNA-specific regulatory programs
## Comparison 1: lncRNA promoters vs protein-coding-gene promoters (reported at Koyo Meeting)
## Comparison 2: promoters of cis-acting vs trans-acting lncRNAs (To Do)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome to identify possible candidates important to the transcriptional network

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse VS human for samples available in both species. Because lncRNAs are less conserved than protein-coding genes, it is possible that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken. There are three specific kinds of conservation that we are interested in analyzing: i) sequence (using UCSC TransMap and liftOver), ii) gene structure (location and presence/absence in the genome of lncRNAs; including chain conservation), iii) expression.

Specific tasks:
# (?) mapping human lncRNAs to mouse (TransMap/liftOver)
## (?) sequence conservation (-500/+500 TSS promoter regions vs. exons of full-length transcripts)
### (?) frequency
### (?) relative cis- vs. trans- conservation
### (?) promoter regions vs. full-length of transcripts
## (?) conservation of gene structure between the lncRNA genome location in human and the orthologous locus in mouse
### (?) presence/absence of lncRNAs (e.g. present in human, absent in mouse; but nearby known genes are conserved)
### (?) Positional Equivalents (Engstrom et al 2006 FANTOM3 definition)
#### (?) genomewide discovery of tag-only Positional Equivalents (human: cDNA/EST and hCAGE support; mouse: hCAGE-only support)
### (?) relative cis- vs. trans- conservation (QUESTION: How will we approach this? - LL)
### (?) conservation and partial conservation of the chainome
## (?) expression conservation
### (?) performed for conserved matches identified in 1.1 and also for conserved chains identified in 1.2
# (Yulia for global analysis, Leonard for annotation) frequency OF REPEAT-initiated TSS in lncRNA in humans vs. mouse (QUESTION: Do we have, or need, RNAseq/CAGEscan data from mouse for this? - LL)

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target cis-networks involving transcription of transcription factor or epigenetic modifier genes that are antisense to lncRNAs (in pairs or chains)
# (Max? Harukazu? WP6?) Which of these loci already have lncRNA-mRNA cis-co-expression (of a pair or of at least some part of a chain) in any of the cell line systems that are available for validation? What cell lines can we choose from?
# (coordinated by Harukazu, WP6) knockdown of lncRNAs, measuring local influence of lncRNAs to identify candidates for genome-wide perturbation experiments
## (WP6) probing transcriptional network perturbations through knockdown CAGE-seq
# (WP6) look into feasibility of overexpression experiments
## (Matthias Harbers) provide RIKEN / KK DNAFORM Clone IDs matching the lncRNAs that we may want to overexpress

==Structure features/subclassification of lncRNAs==
The intention here is to provide a classification of lncRNAs based on structural features (including computational secondary structure prediction and overlap with other genomic features) with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, recapping, positioning relative to other genome markers, etc.)

# (Eivind, Max, Helen) overlap with short RNA (TSS-based and other processing products), see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
# (?) overlap with other genome features
# (?) RNA-seq and splicing frequency
# (Hui Jia, Ben Brown) translational potential (small reading frames; overlap all exonic lncRNA sequences from the combined F5 lncRNAome -vs- public ENCODE proteogenomic data, and list all lncRNAs that are either mis-classified mRNAs or have evidence of ectopic translation)
# (CBRC) secondary structure of lncRNAs (NOTE: It is very important to use tools that do not primarily rely on conservation. - LL)
## small-RNA-like (pre-miRNA? piRNA-like? others?) structures (hairpins) and known-ncRNA like (tRNA-like?) structures (stems/loops) in all F5 cDNA/EST, RNAseq, and CAGEscan lncRNA sequences
### overlap of these predicted structures, if any, with known (UCSC sno/miRNA, tRNA etc tracks) small RNAs
## prediction of novel secondary structures specific to the long RNAs, including but not limited to pseudoknots; identification of novel structural lncRNAs that do not function by processing into shorter RNAs
## structure differences that correlate with our different lncRNA classifications (cis- vs trans-, chain vs. non-chain, convergent vs divergent structure in SASpairs, spliced lncRNAs vs. single-exon lncRNAs, known-shortRNA-containing vs non-containing, etc.)

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest, transcribed from enhancers (which act cryptically as lncRNA promoters) and involved in spatial and epigenetic cis-regulation of nearby and distant target genes. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

(BASIC QUESTION: Since eRNAs are polyA-, how do we look for them in F5 data? Which F5 datasets - hCAGE, RNAseq, CAGEscan, some subsets or all of these - retain polyA- transcripts? - LL)

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.) (HOW DO WE KNOW THIS FROM F5 DATA WHICH IS INHERENTLY NOT FULL-LENGTH? - LL, I think length distribution will also be dependent on overlap with RNA-seq, other statistics could include length between eRNA and nearest promoter, etc. - Max)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations
#(Leonard) curation of polyA+ cDNA/EST data suggesting polyA+ lncRNA transcription from loci that also give rise to polyA- eRNAs (e.g. EVF-2 locus DLX5/6 enhancer, and its paralogous locus DLX1/2 enhancer, clearly give rise to polyA+ lncRNAs in cDNA/EST data)

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
## How about specific identification of F5 lncRNAs in disease regions where no causative genes have yet been identified, and using these RNAs' expression profiles from F5 to make the case for their relevance to the particular disease/s? - LL
# (Leonard, Alka) Rett Syndrome and cis-chains
## clinical and translational relevance of the F5 lncRNAome: putative antisense eRNAs in a Rett region precisely recapitulate the exact brain expression profile of a leading Rett candidate gene
## Alka: inclusion of any info on patient deletions of this region depends on approval from and inclusion of your clinical collaborators - LL

==miRNA promoters: Please move this to Satellite page, or explain how it fits into the main paper :-) ==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) definition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Al and Max list of available experimental systems to Leonard
* Current best targets from Emily and Leonard sent to the OSC (Max and Al).
** Max and Al--> discussion with WP6.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome
** Lukasz perform listed tasks
*** listed tasks are performed again on classified cis-acting and trans-acting lncRNAs, looking for differences
* novel lncRNAs are added to the set
** potentially repeat above analyses

==General functional classification of lncRNAs==
* Nicolas cis-acting classification
** Leonard annotation of formal "Chainome"
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
** Leonard / Hui: basic identification of F5 lncRNAs that do, and don't, overlap any known small RNAs (miRNAs, snoRNAs, piwiRNAs)
*** identification of all lncRNAs that lack the potential to function as host of any known small RNAs
*** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two
* construction of the Alu element-containing mRNA list
** Yulia Alu elements role in trans-acting lncRNA gene-targeted expression

==Motif enrichment in promoter regions of lncRNAs==
* Boris motif enrichment
* Michiel MARA

==lncRNA conservation in matching mouse primary cells==
* Al matched human/mouse samples
* Leonard assists in defining determinants of lncRNA conservation
** list of mouse/human sequence conserved sites
** ? sequence conservation
** ? genome structure conservation (includes chains)
*** expression conservation human/mouse based on conserved pairs identified in above two points
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
* ? compilation of conservation statistics (e.g. frequency, etc...)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* Eivind Max Helen overlap with short RNA see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
* CRBC general structural features of identified classes of lncRNAs
* take list of lncRNAs with overlapping short RNAs from above
** CRBC identification of "precursor" structure from RNA-seq and short RNA
** CRBC secondary structure predictions of lncRNAs in short RNA regions
*** CRBC integration of the two above

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation

==lncRNA and human disease overlap==
* Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* Leonard and Alka pursue Rhett story

Long noncoding RNA main paper

2011-11-07T05:04:51Z

Burrough: /* miRNA promoters: Please move this to Satellite page, or explain how it fits into the main paper :-) */

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see the Noncoding RNA central [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Noncoding_RNA_central_page#RNA-seq page]. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives, leadership, and communication=
This paper aims to capture, and functionally define, the complete breadth and diversity of the non-redundant set of long noncoding RNA (lncRNA) genes in the human genome, while leveraging the unique qualities of FANTOM5 (hCAGE, RNAseq, >1k human cell and tissue samples) to fully characterize the cell type specificity, timecourse responsiveness, regulatory network participation, and evolutionary impact of these genes. For the purpose of this paper, it is important to note that our definition of lncRNAs is broader than that used by others, and includes, in addition to lincRNAs (long intergenic ncRNAs), all bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE, RNAseq, and/or pre-F5 cDNA/EST support. In addition, this paper will use genome organization and context coupled with hCAGE-measured expression of coding genes to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

Paper leadership:
# Max Burroughs, Nicolas Bertin - listed first authors; main OSC contacts
# Leonard Lipovich - listed last (principal) author; key coordinator
# Al / Piero / WP4 / WP6 - overall supervision and co-direction; procurement and organization of datasets and validations.

Communication: We will have specific lncRNA main paper TeleConference calls (times TBD). These are different from the main F5 TCs.

=Tasks for the paper=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Koyo meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks will end up as satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. We are currently updating the non-redundant gene-centric human lncRNA catalog ("the F5 lncRNAome") with RNAs from Cabili et al Genes & Dev 2011. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard, Hui) Generation of the definitive gene-centric non-redundant FANTOM5 lncRNAome: "the" human lncRNA catalog
## (Leonard, Hui) Inclusion of latest lncRNAs from the Cabili et al and the Gencode lncRNA Derrien et al papers - done
## (Leonard, Hui) FUNDAMENTAL CHARACTERIZATION OF THE LNCRNAOME, identifying and counting lncRNAs in each of the following categories:
### standalone spliced lncRNA (consistent with "lincRNA" definition)
### standalone single-exon lncRNA
### lncRNA in a gene pair
#### bidirectionally promoted lncRNA
#### lncRNA nested intronically inside another gene, in the same direction as that gene
#### sense-antisense lncRNA
##### exonic antisense overlap with anothe gene
##### intronic antisense overlap with another gene
## (Max, Leonard, OSC) increasing the non-redundant lncRNAome by incorporating novel transcripts identified through FANTOM5 hCAGE and RNA-seq data - still To Do
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks from UPDATE012 and UPDATE013 associating with lncRNAome from the final filtered and normalized clustering values (Question: Where is the final list of Clusters that we should use for this? - LL)
# (Lukasz, and Tom Freeman!) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and (Tom Freeman?) in different tissues (made available on the wiki to sample providers)
## (Tom Freeman) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz, Win Hide, and Emmanuel Dimont!) Time course expression
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
## (Win, Emmanuel) lncRNAs that go from low to high (or from high to low) in any specific timecourse
## (Win, Emmanuel) complete SwitchEngine analysis of lncRNA expression in timecourses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles (Question: Lukasz, how is this different from Tom F's stuff? - LL)
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)
# (how about Vlad or Boris J here?) tissue-specific differential promoter usage in lncRNAs; comparison to coding differential promoter usage

==General functional classification of lncRNAs==
Here we define the subset of lncRNAs likely to be acting in "cis" based on their genomic proximity to their putative cis-target or co-regulated genes, and develop specific, network-level functional predictions for individual lncRNAs based on co-expression. We also attempt to identify all lncRNAs involved in "trans" regulation (i.e. regulation of genes that reside outside of the lncRNA-encoding locus), and lncRNAs which may function as precursors for small/er RNA biogenesis. While there is some overlap in the analyses, due to the fact that some RNAs are probably involved in more than one of these three functional modalities, they are treated in separate sections below.

===cis-acting lncRNAs===
Specific tasks:
# (Nicolas, Leonard) Preliminary classification of cis-acting lncRNAs
## (Nicolas) calculating (PCC) and ranking sense-antisense co-expression at all ~ 2,800 manually annotated lncRNA-mRNA sense-antisense ("SAS") pairs (from the 4,511-pair F5 SASome provided by Leonard) in latest data updates (012 and 013)
## (Leonard) annotation of the above into a curated set representing top-ranking co-regulated and anti-regulated lncRNA-mRNA SASpairs; emphasis on pairs containing mRNAs that encode transcriptional regulators (will use DAVID, Panther to ID them)
## (Leonard) update of the FANTOM3 human "Chainome" (already obtained from Engstrom et al) to hg19; identification of all lncRNA-containing chains; addition of new lncRNA-containing chains from non-Engstrom sources (Emily) to update the F5 Chainome
# cis-acting lncRNA analysis (each analysis performed on both the lncRNA-containing SASome extracted by Nicolas and the lncRNA-containing chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes (QUESTION: What is "locally-connected?" Are you referring to genomic neighbors here, but to in-trans co-expression or ontology-based connections when this outline item re-appears in the section below on trans-acting lncRNAs? - LL)
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains including both co-expressed gene ontology and cell tree ontology (i.e. co-expression of mRNAs in-cis, and/or of specific ontological categories of mRNAs in-trans, across related cell lineages gives clue to function)
### co-expression patterns to search for include lncRNA chains where all members are expressed; and chains where lncRNA is expressed and mRNA is not, and vice/versa.
## (Michiel) MARA analysis to see influence of cis-acting lncRNAs on transcriptional network (see motif enrichment section below)
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains (QUESTION: What is this? Is it redundant with stuff elsewhere in the outline? - LL)
### similar to above, search for potential effects on expression of chains in presence/absence of small RNA and its orientation
### (Eivind, Helena, Max, Martin, Asai-sensei / CBRC (see structure section below)) lncRNAs serving as possible small RNA precursors, and identification of novel structures in long RNAs

===trans-acting lncRNAs===
# (all) identification of potential trans-acting lncRNAs and their classes (classes: general trans-acting, Alu-element acting, and short RNA precursor transcripts)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
## (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results
## (Yulia) direct/inverse co-expression patterns of lncRNAs with known-gene mRNAs with Alu elements in 3'UTRs (based on Gong and Maquat 2011 Nature paper)
### (Hui, Leonard may assist w/ this) requires construction of the set of mRNAs with Alu elements in the 3' UTR to specifically look at effects of expression in these lncRNAs/potential target mRNAs
## (?) identification of all lncRNAs that are cis-antisense to pseudogenes and that therefore may regulate in-trans the parental genes of the pseudogenes (check recent papers by Kevin Morris, this is a very "hot" area that we must cover)

===RNA processing of the F5 lncRNAome: empirical evidence from hCAGE/RNAseq/CAGEscan integration===
# RNA processing at exonic sense-antisense overlaps of lncRNA-mRNA pairs
## Cleavage and 5' capping of putative 3' cleavage fragments that map to SAS overlaps: capped (hCAGE and CAGEscan) data
### (Leonard) Case study: BDNF/BDNFOS (asymmetric capped cleavage products, symmetric uncapped short RNAs from SAS overlap)
### (?) Global analysis: Which of our ~ 2,800 annotated SAS overlaps give rise to capped? uncapped? symmetric? asymmetric? both?
# RNA processing of lncRNAs that serve as hosts of functional short RNAs
## Cleavage and 5' capping of 3' cleavage fragments located within the host lncRNA and after the mature short RNA sequence
### (Leonard) Case study: AK044422
# Human-mouse non-conservation of RNA processing: orthologous mouse loci that do not recapitulate the human pattern of capping and polarity (e.g. Bdnf); orthologous human loci that do not recapitulate the mouse pattern of cleave-and-cap after miRNA sequences (AK044422)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
## (Nicolas) Use CAGE-scan to look specifically for lncRNA TSSs inside repeats
## (Nicolas, Max) tabulation of all novel lncRNAs from this data and incorporation into non-redundant lncRNAome
# (Leonard, Hui) nonredundant incorporation of the combined data into the F5 lncRNAome: Go To Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset, task 1, subtask 3
# (Laurens) annotation of a set of novel lncRNAs (Question: Which set? Can Laurens annotate the novel RNAseq/CAGEscan hits, or was the original plan to rely on the HAVANA annotation of other F5 lncRNAome entries that was presented at the Koyo Meeting? - LL)

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Motif enrichment and lncRNA-specific regulatory programs
## Comparison 1: lncRNA promoters vs protein-coding-gene promoters (reported at Koyo Meeting)
## Comparison 2: promoters of cis-acting vs trans-acting lncRNAs (To Do)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome to identify possible candidates important to the transcriptional network

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse VS human for samples available in both species. Because lncRNAs are less conserved than protein-coding genes, it is possible that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken. There are three specific kinds of conservation that we are interested in analyzing: i) sequence (using UCSC TransMap and liftOver), ii) gene structure (location and presence/absence in the genome of lncRNAs; including chain conservation), iii) expression.

Specific tasks:
# (?) mapping human lncRNAs to mouse (TransMap/liftOver)
## (?) sequence conservation (-500/+500 TSS promoter regions vs. exons of full-length transcripts)
### (?) frequency
### (?) relative cis- vs. trans- conservation
### (?) promoter regions vs. full-length of transcripts
## (?) conservation of gene structure between the lncRNA genome location in human and the orthologous locus in mouse
### (?) presence/absence of lncRNAs (e.g. present in human, absent in mouse; but nearby known genes are conserved)
### (?) Positional Equivalents (Engstrom et al 2006 FANTOM3 definition)
#### (?) genomewide discovery of tag-only Positional Equivalents (human: cDNA/EST and hCAGE support; mouse: hCAGE-only support)
### (?) relative cis- vs. trans- conservation (QUESTION: How will we approach this? - LL)
### (?) conservation and partial conservation of the chainome
## (?) expression conservation
### (?) performed for conserved matches identified in 1.1 and also for conserved chains identified in 1.2
# (Yulia for global analysis, Leonard for annotation) frequency OF REPEAT-initiated TSS in lncRNA in humans vs. mouse (QUESTION: Do we have, or need, RNAseq/CAGEscan data from mouse for this? - LL)

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target cis-networks involving transcription of transcription factor or epigenetic modifier genes that are antisense to lncRNAs (in pairs or chains)
# (Max? Harukazu? WP6?) Which of these loci already have lncRNA-mRNA cis-co-expression (of a pair or of at least some part of a chain) in any of the cell line systems that are available for validation? What cell lines can we choose from?
# (coordinated by Harukazu, WP6) knockdown of lncRNAs, measuring local influence of lncRNAs to identify candidates for genome-wide perturbation experiments
## (WP6) probing transcriptional network perturbations through knockdown CAGE-seq
# (WP6) look into feasibility of overexpression experiments
## (Matthias Harbers) provide RIKEN / KK DNAFORM Clone IDs matching the lncRNAs that we may want to overexpress

==Structure features/subclassification of lncRNAs==
The intention here is to provide a classification of lncRNAs based on structural features (including computational secondary structure prediction and overlap with other genomic features) with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, recapping, positioning relative to other genome markers, etc.)

# (Eivind, Max, Helen) overlap with short RNA (TSS-based and other processing products), see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
# (?) overlap with other genome features
# (?) RNA-seq and splicing frequency
# (Hui Jia, Ben Brown) translational potential (small reading frames; overlap all exonic lncRNA sequences from the combined F5 lncRNAome -vs- public ENCODE proteogenomic data, and list all lncRNAs that are either mis-classified mRNAs or have evidence of ectopic translation)
# (CBRC) secondary structure of lncRNAs (NOTE: It is very important to use tools that do not primarily rely on conservation. - LL)
## small-RNA-like (pre-miRNA? piRNA-like? others?) structures (hairpins) and known-ncRNA like (tRNA-like?) structures (stems/loops) in all F5 cDNA/EST, RNAseq, and CAGEscan lncRNA sequences
### overlap of these predicted structures, if any, with known (UCSC sno/miRNA, tRNA etc tracks) small RNAs
## prediction of novel secondary structures specific to the long RNAs, including but not limited to pseudoknots; identification of novel structural lncRNAs that do not function by processing into shorter RNAs
## structure differences that correlate with our different lncRNA classifications (cis- vs trans-, chain vs. non-chain, convergent vs divergent structure in SASpairs, spliced lncRNAs vs. single-exon lncRNAs, known-shortRNA-containing vs non-containing, etc.)

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest, transcribed from enhancers (which act cryptically as lncRNA promoters) and involved in spatial and epigenetic cis-regulation of nearby and distant target genes. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

(BASIC QUESTION: Since eRNAs are polyA-, how do we look for them in F5 data? Which F5 datasets - hCAGE, RNAseq, CAGEscan, some subsets or all of these - retain polyA- transcripts? - LL)

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.) (HOW DO WE KNOW THIS FROM F5 DATA WHICH IS INHERENTLY NOT FULL-LENGTH? - LL)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations
#(Leonard) curation of polyA+ cDNA/EST data suggesting polyA+ lncRNA transcription from loci that also give rise to polyA- eRNAs (e.g. EVF-2 locus DLX5/6 enhancer, and its paralogous locus DLX1/2 enhancer, clearly give rise to polyA+ lncRNAs in cDNA/EST data)

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
## How about specific identification of F5 lncRNAs in disease regions where no causative genes have yet been identified, and using these RNAs' expression profiles from F5 to make the case for their relevance to the particular disease/s? - LL
# (Leonard, Alka) Rett Syndrome and cis-chains
## clinical and translational relevance of the F5 lncRNAome: putative antisense eRNAs in a Rett region precisely recapitulate the exact brain expression profile of a leading Rett candidate gene
## Alka: inclusion of any info on patient deletions of this region depends on approval from and inclusion of your clinical collaborators - LL

==miRNA promoters: Please move this to Satellite page, or explain how it fits into the main paper :-) ==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) definition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Al and Max list of available experimental systems to Leonard
* Current best targets from Emily and Leonard sent to the OSC (Max and Al).
** Max and Al--> discussion with WP6.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome
** Lukasz perform listed tasks
*** listed tasks are performed again on classified cis-acting and trans-acting lncRNAs, looking for differences
* novel lncRNAs are added to the set
** potentially repeat above analyses

==General functional classification of lncRNAs==
* Nicolas cis-acting classification
** Leonard annotation of formal "Chainome"
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
** Leonard / Hui: basic identification of F5 lncRNAs that do, and don't, overlap any known small RNAs (miRNAs, snoRNAs, piwiRNAs)
*** identification of all lncRNAs that lack the potential to function as host of any known small RNAs
*** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two
* construction of the Alu element-containing mRNA list
** Yulia Alu elements role in trans-acting lncRNA gene-targeted expression

==Motif enrichment in promoter regions of lncRNAs==
* Boris motif enrichment
* Michiel MARA

==lncRNA conservation in matching mouse primary cells==
* Al matched human/mouse samples
* Leonard assists in defining determinants of lncRNA conservation
** list of mouse/human sequence conserved sites
** ? sequence conservation
** ? genome structure conservation (includes chains)
*** expression conservation human/mouse based on conserved pairs identified in above two points
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
* ? compilation of conservation statistics (e.g. frequency, etc...)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* Eivind Max Helen overlap with short RNA see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
* CRBC general structural features of identified classes of lncRNAs
* take list of lncRNAs with overlapping short RNAs from above
** CRBC identification of "precursor" structure from RNA-seq and short RNA
** CRBC secondary structure predictions of lncRNAs in short RNA regions
*** CRBC integration of the two above

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation

==lncRNA and human disease overlap==
* Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* Leonard and Alka pursue Rhett story

Long noncoding RNA main paper

2011-11-07T04:57:21Z

Burrough: /* Paper objectives, leadership, and communication */

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see the Noncoding RNA central [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Noncoding_RNA_central_page#RNA-seq page]. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives, leadership, and communication=
This paper aims to capture, and functionally define, the complete breadth and diversity of the non-redundant set of long noncoding RNA (lncRNA) genes in the human genome, while leveraging the unique qualities of FANTOM5 (hCAGE, RNAseq, >1k human cell and tissue samples) to fully characterize the cell type specificity, timecourse responsiveness, regulatory network participation, and evolutionary impact of these genes. For the purpose of this paper, it is important to note that our definition of lncRNAs is broader than that used by others, and includes, in addition to lincRNAs (long intergenic ncRNAs), all bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE, RNAseq, and/or pre-F5 cDNA/EST support. In addition, this paper will use genome organization and context coupled with hCAGE-measured expression of coding genes to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

Paper leadership:
# Max Burroughs, Nicolas Bertin - listed first authors; main OSC contacts
# Leonard Lipovich - listed last (principal) author; key coordinator
# Al / Piero / WP4 / WP6 - overall supervision and co-direction; procurement and organization of datasets and validations.

Communication: We will have specific lncRNA main paper TeleConference calls (times TBD). These are different from the main F5 TCs.

=Tasks for the paper=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Koyo meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks will end up as satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. We are currently updating the non-redundant gene-centric human lncRNA catalog ("the F5 lncRNAome") with RNAs from Cabili et al Genes & Dev 2011. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard, Hui) Generation of the definitive gene-centric non-redundant FANTOM5 lncRNAome: "the" human lncRNA catalog
## (Leonard, Hui) Inclusion of latest lncRNAs from the Cabili et al and the Gencode lncRNA Derrien et al papers - done
## (Leonard, Hui) FUNDAMENTAL CHARACTERIZATION OF THE LNCRNAOME, identifying and counting lncRNAs in each of the following categories:
### standalone spliced lncRNA (consistent with "lincRNA" definition)
### standalone single-exon lncRNA
### lncRNA in a gene pair
#### bidirectionally promoted lncRNA
#### lncRNA nested intronically inside another gene, in the same direction as that gene
#### sense-antisense lncRNA
##### exonic antisense overlap with anothe gene
##### intronic antisense overlap with another gene
## (Max, Leonard, OSC) increasing the non-redundant lncRNAome by incorporating novel transcripts identified through FANTOM5 hCAGE and RNA-seq data - still To Do
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks from UPDATE012 and UPDATE013 associating with lncRNAome from the final filtered and normalized clustering values (Question: Where is the final list of Clusters that we should use for this? - LL)
# (Lukasz, and Tom Freeman!) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and (Tom Freeman?) in different tissues (made available on the wiki to sample providers)
## (Tom Freeman) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz, Win Hide, and Emmanuel Dimont!) Time course expression
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
## (Win, Emmanuel) lncRNAs that go from low to high (or from high to low) in any specific timecourse
## (Win, Emmanuel) complete SwitchEngine analysis of lncRNA expression in timecourses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles (Question: Lukasz, how is this different from Tom F's stuff? - LL)
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)
# (how about Vlad or Boris J here?) tissue-specific differential promoter usage in lncRNAs; comparison to coding differential promoter usage

==General functional classification of lncRNAs==
Here we define the subset of lncRNAs likely to be acting in "cis" based on their genomic proximity to their putative cis-target or co-regulated genes, and develop specific, network-level functional predictions for individual lncRNAs based on co-expression. We also attempt to identify all lncRNAs involved in "trans" regulation (i.e. regulation of genes that reside outside of the lncRNA-encoding locus), and lncRNAs which may function as precursors for small/er RNA biogenesis. While there is some overlap in the analyses, due to the fact that some RNAs are probably involved in more than one of these three functional modalities, they are treated in separate sections below.

===cis-acting lncRNAs===
Specific tasks:
# (Nicolas, Leonard) Preliminary classification of cis-acting lncRNAs
## (Nicolas) calculating (PCC) and ranking sense-antisense co-expression at all ~ 2,800 manually annotated lncRNA-mRNA sense-antisense ("SAS") pairs (from the 4,511-pair F5 SASome provided by Leonard) in latest data updates (012 and 013)
## (Leonard) annotation of the above into a curated set representing top-ranking co-regulated and anti-regulated lncRNA-mRNA SASpairs; emphasis on pairs containing mRNAs that encode transcriptional regulators (will use DAVID, Panther to ID them)
## (Leonard) update of the FANTOM3 human "Chainome" (already obtained from Engstrom et al) to hg19; identification of all lncRNA-containing chains; addition of new lncRNA-containing chains from non-Engstrom sources (Emily) to update the F5 Chainome
# cis-acting lncRNA analysis (each analysis performed on both the lncRNA-containing SASome extracted by Nicolas and the lncRNA-containing chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes (QUESTION: What is "locally-connected?" Are you referring to genomic neighbors here, but to in-trans co-expression or ontology-based connections when this outline item re-appears in the section below on trans-acting lncRNAs? - LL)
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains including both co-expressed gene ontology and cell tree ontology (i.e. co-expression of mRNAs in-cis, and/or of specific ontological categories of mRNAs in-trans, across related cell lineages gives clue to function)
### co-expression patterns to search for include lncRNA chains where all members are expressed; and chains where lncRNA is expressed and mRNA is not, and vice/versa.
## (Michiel) MARA analysis to see influence of cis-acting lncRNAs on transcriptional network (see motif enrichment section below)
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains (QUESTION: What is this? Is it redundant with stuff elsewhere in the outline? - LL)
### similar to above, search for potential effects on expression of chains in presence/absence of small RNA and its orientation
### (Eivind, Helena, Max, Martin, Asai-sensei / CBRC (see structure section below)) lncRNAs serving as possible small RNA precursors, and identification of novel structures in long RNAs

===trans-acting lncRNAs===
# (all) identification of potential trans-acting lncRNAs and their classes (classes: general trans-acting, Alu-element acting, and short RNA precursor transcripts)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
## (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results
## (Yulia) direct/inverse co-expression patterns of lncRNAs with known-gene mRNAs with Alu elements in 3'UTRs (based on Gong and Maquat 2011 Nature paper)
### (Hui, Leonard may assist w/ this) requires construction of the set of mRNAs with Alu elements in the 3' UTR to specifically look at effects of expression in these lncRNAs/potential target mRNAs
## (?) identification of all lncRNAs that are cis-antisense to pseudogenes and that therefore may regulate in-trans the parental genes of the pseudogenes (check recent papers by Kevin Morris, this is a very "hot" area that we must cover)

===RNA processing of the F5 lncRNAome: empirical evidence from hCAGE/RNAseq/CAGEscan integration===
# RNA processing at exonic sense-antisense overlaps of lncRNA-mRNA pairs
## Cleavage and 5' capping of putative 3' cleavage fragments that map to SAS overlaps: capped (hCAGE and CAGEscan) data
### (Leonard) Case study: BDNF/BDNFOS (asymmetric capped cleavage products, symmetric uncapped short RNAs from SAS overlap)
### (?) Global analysis: Which of our ~ 2,800 annotated SAS overlaps give rise to capped? uncapped? symmetric? asymmetric? both?
# RNA processing of lncRNAs that serve as hosts of functional short RNAs
## Cleavage and 5' capping of 3' cleavage fragments located within the host lncRNA and after the mature short RNA sequence
### (Leonard) Case study: AK044422
# Human-mouse non-conservation of RNA processing: orthologous mouse loci that do not recapitulate the human pattern of capping and polarity (e.g. Bdnf); orthologous human loci that do not recapitulate the mouse pattern of cleave-and-cap after miRNA sequences (AK044422)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
## (Nicolas) Use CAGE-scan to look specifically for lncRNA TSSs inside repeats
## (Nicolas, Max) tabulation of all novel lncRNAs from this data and incorporation into non-redundant lncRNAome
# (Leonard, Hui) nonredundant incorporation of the combined data into the F5 lncRNAome: Go To Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset, task 1, subtask 3
# (Laurens) annotation of a set of novel lncRNAs (Question: Which set? Can Laurens annotate the novel RNAseq/CAGEscan hits, or was the original plan to rely on the HAVANA annotation of other F5 lncRNAome entries that was presented at the Koyo Meeting? - LL)

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Motif enrichment and lncRNA-specific regulatory programs
## Comparison 1: lncRNA promoters vs protein-coding-gene promoters (reported at Koyo Meeting)
## Comparison 2: promoters of cis-acting vs trans-acting lncRNAs (To Do)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome to identify possible candidates important to the transcriptional network

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse VS human for samples available in both species. Because lncRNAs are less conserved than protein-coding genes, it is possible that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken. There are three specific kinds of conservation that we are interested in analyzing: i) sequence (using UCSC TransMap and liftOver), ii) gene structure (location and presence/absence in the genome of lncRNAs; including chain conservation), iii) expression.

Specific tasks:
# (?) mapping human lncRNAs to mouse (TransMap/liftOver)
## (?) sequence conservation (-500/+500 TSS promoter regions vs. exons of full-length transcripts)
### (?) frequency
### (?) relative cis- vs. trans- conservation
### (?) promoter regions vs. full-length of transcripts
## (?) conservation of gene structure between the lncRNA genome location in human and the orthologous locus in mouse
### (?) presence/absence of lncRNAs (e.g. present in human, absent in mouse; but nearby known genes are conserved)
### (?) Positional Equivalents (Engstrom et al 2006 FANTOM3 definition)
#### (?) genomewide discovery of tag-only Positional Equivalents (human: cDNA/EST and hCAGE support; mouse: hCAGE-only support)
### (?) relative cis- vs. trans- conservation (QUESTION: How will we approach this? - LL)
### (?) conservation and partial conservation of the chainome
## (?) expression conservation
### (?) performed for conserved matches identified in 1.1 and also for conserved chains identified in 1.2
# (Yulia for global analysis, Leonard for annotation) frequency OF REPEAT-initiated TSS in lncRNA in humans vs. mouse (QUESTION: Do we have, or need, RNAseq/CAGEscan data from mouse for this? - LL)

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target cis-networks involving transcription of transcription factor or epigenetic modifier genes that are antisense to lncRNAs (in pairs or chains)
# (Max? Harukazu? WP6?) Which of these loci already have lncRNA-mRNA cis-co-expression (of a pair or of at least some part of a chain) in any of the cell line systems that are available for validation? What cell lines can we choose from?
# (coordinated by Harukazu, WP6) knockdown of lncRNAs, measuring local influence of lncRNAs to identify candidates for genome-wide perturbation experiments
## (WP6) probing transcriptional network perturbations through knockdown CAGE-seq
# (WP6) look into feasibility of overexpression experiments
## (Matthias Harbers) provide RIKEN / KK DNAFORM Clone IDs matching the lncRNAs that we may want to overexpress

==Structure features/subclassification of lncRNAs==
The intention here is to provide a classification of lncRNAs based on structural features (including computational secondary structure prediction and overlap with other genomic features) with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, recapping, positioning relative to other genome markers, etc.)

# (Eivind, Max, Helen) overlap with short RNA (TSS-based and other processing products), see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
# (?) overlap with other genome features
# (?) RNA-seq and splicing frequency
# (Hui Jia, Ben Brown) translational potential (small reading frames; overlap all exonic lncRNA sequences from the combined F5 lncRNAome -vs- public ENCODE proteogenomic data, and list all lncRNAs that are either mis-classified mRNAs or have evidence of ectopic translation)
# (CBRC) secondary structure of lncRNAs (NOTE: It is very important to use tools that do not primarily rely on conservation. - LL)
## small-RNA-like (pre-miRNA? piRNA-like? others?) structures (hairpins) and known-ncRNA like (tRNA-like?) structures (stems/loops) in all F5 cDNA/EST, RNAseq, and CAGEscan lncRNA sequences
### overlap of these predicted structures, if any, with known (UCSC sno/miRNA, tRNA etc tracks) small RNAs
## prediction of novel secondary structures specific to the long RNAs, including but not limited to pseudoknots; identification of novel structural lncRNAs that do not function by processing into shorter RNAs
## structure differences that correlate with our different lncRNA classifications (cis- vs trans-, chain vs. non-chain, convergent vs divergent structure in SASpairs, spliced lncRNAs vs. single-exon lncRNAs, known-shortRNA-containing vs non-containing, etc.)

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest, transcribed from enhancers (which act cryptically as lncRNA promoters) and involved in spatial and epigenetic cis-regulation of nearby and distant target genes. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

(BASIC QUESTION: Since eRNAs are polyA-, how do we look for them in F5 data? Which F5 datasets - hCAGE, RNAseq, CAGEscan, some subsets or all of these - retain polyA- transcripts? - LL)

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.) (HOW DO WE KNOW THIS FROM F5 DATA WHICH IS INHERENTLY NOT FULL-LENGTH? - LL)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations
#(Leonard) curation of polyA+ cDNA/EST data suggesting polyA+ lncRNA transcription from loci that also give rise to polyA- eRNAs (e.g. EVF-2 locus DLX5/6 enhancer, and its paralogous locus DLX1/2 enhancer, clearly give rise to polyA+ lncRNAs in cDNA/EST data)

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
## How about specific identification of F5 lncRNAs in disease regions where no causative genes have yet been identified, and using these RNAs' expression profiles from F5 to make the case for their relevance to the particular disease/s? - LL
# (Leonard, Alka) Rett Syndrome and cis-chains
## clinical and translational relevance of the F5 lncRNAome: putative antisense eRNAs in a Rett region precisely recapitulate the exact brain expression profile of a leading Rett candidate gene
## Alka: inclusion of any info on patient deletions of this region depends on approval from and inclusion of your clinical collaborators - LL

==miRNA promoters: Please move this to Satellite page, or explain how it fits into the main paper :-) ==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) idefinition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Al and Max list of available experimental systems to Leonard
* Current best targets from Emily and Leonard sent to the OSC (Max and Al).
** Max and Al--> discussion with WP6.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome
** Lukasz perform listed tasks
*** listed tasks are performed again on classified cis-acting and trans-acting lncRNAs, looking for differences
* novel lncRNAs are added to the set
** potentially repeat above analyses

==General functional classification of lncRNAs==
* Nicolas cis-acting classification
** Leonard annotation of formal "Chainome"
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
** Leonard / Hui: basic identification of F5 lncRNAs that do, and don't, overlap any known small RNAs (miRNAs, snoRNAs, piwiRNAs)
*** identification of all lncRNAs that lack the potential to function as host of any known small RNAs
*** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two
* construction of the Alu element-containing mRNA list
** Yulia Alu elements role in trans-acting lncRNA gene-targeted expression

==Motif enrichment in promoter regions of lncRNAs==
* Boris motif enrichment
* Michiel MARA

==lncRNA conservation in matching mouse primary cells==
* Al matched human/mouse samples
* Leonard assists in defining determinants of lncRNA conservation
** list of mouse/human sequence conserved sites
** ? sequence conservation
** ? genome structure conservation (includes chains)
*** expression conservation human/mouse based on conserved pairs identified in above two points
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
* ? compilation of conservation statistics (e.g. frequency, etc...)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* Eivind Max Helen overlap with short RNA see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
* CRBC general structural features of identified classes of lncRNAs
* take list of lncRNAs with overlapping short RNAs from above
** CRBC identification of "precursor" structure from RNA-seq and short RNA
** CRBC secondary structure predictions of lncRNAs in short RNA regions
*** CRBC integration of the two above

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation

==lncRNA and human disease overlap==
* Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* Leonard and Alka pursue Rhett story

Noncoding RNA central page

2011-11-04T05:14:34Z

Burrough:

Noncoding RNA central page

2011-11-04T05:12:56Z

Burrough: /* ZENBU configuration */

Noncoding RNA central page

2011-11-04T05:07:03Z

Burrough:

Long noncoding RNA main paper

2011-11-04T04:41:28Z

Burrough:

FANTOM5 RNA-seq

2011-11-04T04:39:52Z

Burrough:

Welcome to the FANTOM5 RNA-seq analysis page. This page is intended to document efforts to incorporate RNA-seq into the FANTOM5 project at large. The need for RNA-seq in FANTOM5 was conceived as a means of discerning the nature of novel peaks first identified in the hCAGE data. The initial target of these efforts is providing supplementary data for the long noncoding RNA (lncRNA) and possibly promoterome main papers. As such, if all goes well we intend for much of this analysis to be folded into the lncRNA main paper.

=Specific tasks=
# selection of FANTOM5 samples for RNA-seq, sequencing, RNA-seq processing, and transcript assembly (Al, Max, RIKEN OSC)
# collection and formatting of publicly-available RNA-seq data for further assistance in 'validation' (Max, open to recommendations)
# establish guidelines to determine inclusion as novel lncRNA
# incorporate novel lncRNAs into main dataset
# classification of lncRNAs incorporating RNA-seq data

=Progress=

==Task #1==
Selection of samples:
Here is the list [[File:F5_RNAseq_library_list.xlsx‎]] of samples selected for FANTOM5 RNA-seq. The selection criteria was simple: samples enabling the sequencing of the largest number of novel peaks based on the hCAGE data for the minimum number of samples were chosen.
Sequencing:
Currently library construction is underway. Sequencing will begin upon finishing, hopefully finishing at the end of December.
RNA-seq processing:
to be updated.
Transcript assembly:
to be updated.

==Task #2 (public RNA-seq)==
(Max) Libraries targeted for collection:
# David Brawan et.al. set from "The evolution of gene expression levels in mammalian organs", PMID: 22012392 (polyA, directional?)
# Cabili et.al. set from "Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses", PMID: 21890647 (polyA, directional)
# Illumina BodyMap2 (polyA, directional)
# other large sets (suggestions, pointers welcome)

==Task #3 (establish guidelines to determine inclusion as novel lncRNA)==
Peaks have already been filtered to remove overlap with known coding/non-coding transcripts.
# size of largest open reading frame
# (Jia Hui & Ben Brown) translational analysis to assess coding potential
# size selection?

==Task #4==
(OSC) Incorporation of novel lncRNAs into main dataset

==Task #5 (classification of lncRNAs using RNA-seq & CAGE-scan data)==
# (Eivind, Max, Helen) overlap with short RNA (TSS-based and other processing products), see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
# (?) overlap with other genome features
# (?) splicing
## frequency
## sequence composition at "strong" and "weak" splicing sites
## alternative splicing
# (CBRC) clustering of lncRNA via various metrics
## (CBRC) 2D structural clustering
## (CBRC) 2D structural motif over-representation clustering
## (CBRC) 2D structural accessibility clustering

Long noncoding RNA main paper

2011-11-04T02:50:27Z

Burrough:

Long noncoding RNA main paper

2011-11-04T02:26:53Z

Burrough:

Noncoding RNA central page

2011-11-02T09:44:55Z

Burrough: /* RNA-seq */

FANTOM5 RNA-seq

2011-11-02T09:44:19Z

Burrough:

FANTOM5 RNA-seq

2011-11-02T09:43:56Z

Burrough:

FANTOM5 RNA-seq

2011-11-02T09:43:39Z

Burrough:

File:F5 RNAseq library list.xlsx

2011-11-02T09:42:16Z

Burrough: List of IDs and names of samples selected for RNA-seq.

List of IDs and names of samples selected for RNA-seq.

FANTOM5 RNA-seq

2011-11-02T09:37:15Z

Burrough:

FANTOM5 RNA-seq

2011-11-02T09:30:34Z

Burrough:

Long noncoding RNA main paper

2011-11-02T06:15:54Z

Burrough:

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see this page. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives=
This paper aims to capture the complete breadth and diversity of long noncoding RNAs (lncRNAs) while leveraging the unique qualities of FANTOM5 to understand their cellular restriction and evolutionary impact on the human genome. For the purpose of this paper, it is important to note that our definition of lncRNAs is more broader than others and includes bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE support. In addition, this paper will use genome organization and context to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

=Tasks for the paper=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Kouyou meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks will end up as satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard) Final tweaks to the FANTOM5 lncRNAome
## (Leonard) Inclusion of latest lncRNAs from the Cabili paper (?)
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks associating with lncRNAome from the final filtered and normalized clustering values
# (Lukasz) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and in different tissues (made available on the wiki to sample providers)
## (Lukasz) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz) Time course expression
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)
# (Max, Leonard, OSC) increasing the non-redundant lncRNAome by incorporating novel transcripts identified through FANTOM5 hCAGE and RNA-seq data

==General functional classification of lncRNAs==
Here we are interested in isolating lncRNAs likely to be acting in "cis" and making general functional predictions for individual lncRNAs based on co-expression. We are also interested in probing to what extent we can identify which lncRNAs may be involved in "trans" like regulation and which may primarily function as precursors for small RNA biogenesis. While there is some overlap in the analyses, they are treated in separate sections below.

===cis-acting lncRNAs===
Specific tasks:
# (Nicolas, Leonard) Preliminary classification of cis-acting lncRNAs
## (Nicolas) overlapping sense-antisense co-expression at all lncRNA-mRNA sense-antisense pairs for latest data updates
## (Leonard) annotation of the above into a curated set representing the "Chainome"
# cis-acting lncRNA analysis (each analysis performed on both the complete set extracted by Nicolas and the chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
### co-expression patterns to search for include lncRNA chains where all members are on and chains where lncRNA is on and mRNA is off and vice/versa.
## (Michiel) MARA analysis to see influence of cis-acting lncRNAs on transcriptional network (see motif enrichment section below)
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains
### similar to above, search for potential effects on expression of chains in presence/absence of small RNA and its orientation
### (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors

===trans-acting lncRNAs===
# (all) identification of potential trans-acting lncRNAs and their classes (classes: general trans-acting, Alu-element acting, and short RNA precursor transcripts)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
## (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results
## (Yulia) direct/inverse co-expression patterns of lncRNAs with known-gene mRNAs with Alu elements in 3'UTRs (based on Gong and Maquat 2011 Nature paper)
### requires construction of the set of mRNAs with Alu elements in the 3' UTR to specifically look at effects of expression in these lncRNAs/potential target mRNAs

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
## (Nicolas) Use CAGE-scan to look specifically for lncRNA TSSs inside repeats
## (Nicolas, Max) tabulation of all novel lncRNAs from this data and incorporation into non-redundant lncRNAome
# (Laurens) annotation of set of novel lncRNAs

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Comparisons of motif enrichment (difference in cis- vs. trans- ?)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome to identify possible candidates important to the transcriptional network

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse and human under the assumption that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken. There are three specific kinds of conservation that we are interested in analyzing: i) sequence (using UCSC TransMap and liftOver), ii) structure (location and presence/absence in the genome of lncRNAs; including chain conservation), iii) expression.

Specific tasks:
# (?) mapping human lncRNAs to mouse (TransMap/liftOver)
## sequence conservation (promoter regions vs. full-length)
### frequency
### relative cis- vs. trans- conservation
### promoter regions vs. full-length of transcripts
## conservation of the structure of the genome location in human and matching mouse lncRNAs
### presence/absence of lncRNAs
### relative cis- vs. trans- conservation
### conservation and partial conservation of the chainome
## expression conservation
### performed for conserved matches identified in 1.1 and also for conserved chains identified in 1.2
# (Yulia for global analysis, Leonard for annotation) frequency and conservation of Alu-initiated TSS in lncRNA in humans vs. mouse

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target networks, likely those influencing tf transcription
# (coordinated by Haru, WP6) knockdown of lncRNAs, measuring influence of lncRNAs, probing transcriptional network perturbations

==Structure features/subclassification of lncRNAs==
The intention here is to provide a comprehensive classification of lncRNAs based on structural features (including computational secondary structure prediction and overlap with other genomic features) with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, recapping, positioning relative to other genome markers, etc.)

# (Eivind, Max, Helen) overlap with short RNA (TSS-based and other processing products), see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
# (?) overlap with other genome features
# (?) RNA-seq and splicing frequency
# (Jia, Ben Brown) translational potential (small reading frames)
# (Martin Frith & CBRC) secondary structure of lncRNA based on different classifications (cis- vs trans-, chain vs. non-chain, splicing vs. non-splicing, shortRNA containing-vs non-containing, etc.)

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
# (Leonard,Alka) Rhett syndrome and cis-chain

==miRNA promoters==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) idefinition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Current best targets from Emily and Leonard sent to the OSC (Max and Al).
** Max and Al--> discussion with WP6.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome
** Lukasz perform listed tasks
*** listed tasks are performed again on classified cis-acting and trans-acting lncRNAs, looking for differences
* novel lncRNAs are added to the set
** potentially repeat above analyses

==General functional classification of lncRNAs==
* Nicolas cis-acting classification
** Leonard annotation of formal "Chainome"
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
**** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two
* construction of the Alu element-containing mRNA list
** Yulia Alu elements role in trans-acting lncRNA gene-targeted expression

==Motif enrichment in promoter regions of lncRNAs==
* Boris motif enrichment
* Michiel MARA

==lncRNA conservation in matching mouse primary cells==
* Al matched human/mouse samples
* Leonard assists in defining determinants of lncRNA conservation
** list of mouse/human sequence conserved sites
** ? sequence conservation
** ? genome structure conservation (includes chains)
*** expression conservation human/mouse based on conserved pairs identified in above two points
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
* ? compilation of conservation statistics (e.g. frequency, etc...)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* Eivind Max Helen overlap with short RNA see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
* CRBC general structural features of identified classes of lncRNAs
* take list of lncRNAs with overlapping short RNAs from above
** CRBC identification of "precursor" structure from RNA-seq and short RNA
** CRBC secondary structure predictions of lncRNAs in short RNA regions
*** CRBC integration of the two above

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation

==lncRNA and human disease overlap==
* Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* Leonard and Alka pursue Rhett story

Long noncoding RNA main paper

2011-11-02T05:57:38Z

Burrough:

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see this page. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives=
This paper aims to capture the complete breadth and diversity of long noncoding RNAs (lncRNAs) while leveraging the unique qualities of FANTOM5 to understand their cellular restriction and evolutionary impact on the human genome. For the purpose of this paper, it is important to note that our definition of lncRNAs is more broader than others and includes bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE support. In addition, this paper will use genome organization and context to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

=Tasks for the paper=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Kouyou meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks will end up as satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard) Final tweaks to the FANTOM5 lncRNAome
## (Leonard) Inclusion of latest lncRNAs from the Cabili paper (?)
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks associating with lncRNAome from the final filtered and normalized clustering values
# (Lukasz) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and in different tissues (made available on the wiki to sample providers)
## (Lukasz) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz) Time course expression
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)
# (Max, Leonard, OSC) increasing the non-redundant lncRNAome by incorporating novel transcripts identified through FANTOM5 hCAGE and RNA-seq data

==General functional classification of lncRNAs==
Here we are interested in isolating lncRNAs likely to be acting in "cis" and making general functional predictions for individual lncRNAs based on co-expression. We are also interested in probing to what extent we can identify which lncRNAs may be involved in "trans" like regulation and which may primarily function as precursors for small RNA biogenesis. While there is some overlap in the analyses, they are treated in separate sections below.

===cis-acting lncRNAs===
Specific tasks:
# (Nicolas, Leonard) Preliminary classification of cis-acting lncRNAs
## (Nicolas) overlapping sense-antisense co-expression at all lncRNA-mRNA sense-antisense pairs for latest data updates
## (Leonard) annotation of the above into a curated set representing the "Chainome"
# cis-acting lncRNA analysis (each analysis performed on both the complete set extracted by Nicolas and the chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
### co-expression patterns to search for include lncRNA chains where all members are on and chains where lncRNA is on and mRNA is off and vice/versa.
## (Michiel) MARA analysis to see influence of cis-acting lncRNAs on transcriptional network (see motif enrichment section below)
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains
### similar to above, search for potential effects on expression of chains in presence/absence of small RNA and its orientation
### (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors

===trans-acting lncRNAs===
# (all) identification of potential trans-acting lncRNAs and their classes (classes: general trans-acting, Alu-element acting, and short RNA precursor transcripts)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
## (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results
## (Yulia) direct/inverse co-expression patterns of lncRNAs with known-gene mRNAs with Alu elements in 3'UTRs (based on Gong and Maquat 2011 Nature paper)
### requires construction of the set of mRNAs with Alu elements in the 3' UTR to specifically look at effects of expression in these lncRNAs/potential target mRNAs

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
## (Nicolas) Use CAGE-scan to look specifically for lncRNA TSSs inside repeats
## (Nicolas, Max) tabulation of all novel lncRNAs from this data and incorporation into non-redundant lncRNAome
# (Laurens) annotation of set of novel lncRNAs

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Comparisons of motif enrichment (difference in cis- vs. trans- ?)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome to identify possible candidates important to the transcriptional network

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse and human under the assumption that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken. There are three specific kinds of conservation that we are interested in analyzing: i) sequence (using UCSC TransMap and liftOver), ii) structure (location and presence/absence in the genome of lncRNAs; including chain conservation), iii) expression.

Specific tasks:
# (?) mapping human lncRNAs to mouse (TransMap/liftOver)
## sequence conservation (promoter regions vs. full-length)
### frequency
### relative cis- vs. trans- conservation
### promoter regions vs. full-length of transcripts
## conservation of the structure of the genome location in human and matching mouse lncRNAs
### presence/absence of lncRNAs
### relative cis- vs. trans- conservation
### conservation and partial conservation of the chainome
## expression conservation
### performed for conserved matches identified in 1.1 and also for conserved chains identified in 1.2
# (Yulia for global analysis, Leonard for annotation) frequency and conservation of Alu-initiated TSS in lncRNA in humans vs. mouse

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target networks, likely those influencing tf transcription
# (coordinated by Haru, WP6) knockdown of lncRNAs, measuring influence of lncRNAs, probing transcriptional network perturbations

==Structure features/subclassification of lncRNAs==
The intention here is to provide a comprehensive classification of lncRNAs based on structural features (including computational secondary structure prediction and overlap with other genomic features) with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, recapping, positioning relative to other genome markers, etc.)

# (Eivind, Max, Helen) overlap with short RNA (TSS-based and other processing products), see short RNA [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Short_RNA_paper_page page]
# (?) overlap with other genome features
# (?) RNA-seq and splicing frequency
# (Jia, Ben Brown) translational potential (small reading frames)
# (Martin Frith & CBRC) secondary structure of lncRNA based on different classifications (cis- vs trans-, chain vs. non-chain, splicing vs. non-splicing, shortRNA containing-vs non-containing, etc.)

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
# (Leonard,Alka) Rhett syndrome and cis-chain

==miRNA promoters==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) idefinition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Current best targets from Emily and Leonard sent to the OSC (Max and Al).
** Max and Al--> discussion with WP6.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome
** Lukasz/Nicolas (?) perform listed tasks
*** listed tasks are performed again on the set of predicted cis-acting and trans-acting lncRNAs, looking for differences

==General functional classification of lncRNAs==
* Nicolas cis-acting classification
** Leonard annotation of formal "Chainome"
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
**** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two
* Yulia Alu-S role in trans-acting lncRNAs

==Motif enrichment in promoter regions of lncRNAs==
* Boris motif enrichment
* Michiel MARA

==lncRNA conservation in matching mouse primary cells==
* ? defines determinants of lncRNA conservation
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
** ? conservation in promoter region vs. remaining sequence
* Leonard defines chain conservation
** Nicolas looks at genome-wide conservation of chains

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* CRBC general structural features of identified classes of lncRNAs
* take list of lncRNAs with overlapping short RNAs from above
** CRBC identification of "precursor" structure from RNA-seq and short RNA
** CRBC secondary structure predictions of lncRNAs in short RNA regions
*** CRBC integration of the two above

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation

==lncRNA and human disease overlap==
* Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* Leonard and Alka pursue Rhett story

Long noncoding RNA main paper

2011-11-02T04:38:38Z

Burrough:

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see this page. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives=
This paper aims to capture the complete breadth and diversity of long noncoding RNAs (lncRNAs) while leveraging the unique qualities of FANTOM5 to understand their cellular restriction and evolutionary impact on the human genome. For the purpose of this paper, it is important to note that our definition of lncRNAs is more broader than others and includes bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE support. In addition, this paper will use genome organization and context to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

=Tasks for the paper=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Kouyou meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks will end up as satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard) Final tweaks to the FANTOM5 lncRNAome
## (Leonard) Inclusion of latest lncRNAs from the Cabili paper (?)
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks associating with lncRNAome from the final filtered and normalized clustering values
# (Lukasz) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and in different tissues (made available on the wiki to sample providers)
## (Lukasz) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz) Time course expression
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)

==General functional classification of lncRNAs==
Here we are interested in isolating lncRNAs likely to be acting in "cis" and making general functional predictions for individual lncRNAs based on co-expression. We are also interested in probing to what extent we can identify which lncRNAs may be involved in "trans" like regulation and which may primarily function as precursors for small RNA biogenesis.

Specific tasks:
# (Nicolas, Leonard) Preliminary classification of cis-acting lncRNAs
## (Nicolas) overlapping sense-antisense co-expression at all lncRNA-mRNA sense-antisense pairs for latest data updates
## (Leonard) annotation of the above into a curated set representing the "Chainome"
## (Nicolas, Yulia) identification of potential trans-acting lncRNAs and their classes
# cis-acting lncRNA analysis (each analysis performed on both the complete set extracted by Nicolas and the chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains including both co-expressed gene ontology and cell tree ontology (i.e. co-expression across related cell lineages gives clue to function)
### co-expression patterns to search for include lncRNA chains where all members are on and chains where lncRNA is on and mRNA is off and vice/versa.
## (Michiel) MARA analysis to see influence of cis-acting lncRNAs on transcriptional network (see motif enrichment section below)
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains
### similar to above, search for potential effects on expression of lncRNA and coding RNA in presence/absence of small RNA and its orientation
### (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors
# trans-acting lncRNA analysis
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results
## (Yulia) direct/inverse co-expression patterns of lncRNAs with known-gene mRNAs with Alu-S in 3'UTRs (based on Gong and Maquat 2011 Nature paper)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
# (Laurens) annotation of set of novel lncRNAs

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Comparisons of motif enrichment (difference in cis- vs. trans- ?)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome to identify possible candidates important to the transcriptional network

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse and human under the assumption that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken.

Specific tasks:
# (?) mapping human lncRNAs to mouse (TransMap/liftOver)
# (?) conservation frequency of human-specific lncRNAs in matching mouse primary cells
## (?) relative conservation of cis- and trans- acting
# (?) analysis of sequence conservation; promoter regions vs. the length of the transcript.
# (Leonard talks to Nicolas) conservation of "chainome"
# (Yulia for global analysis, Leonard for annotation) frequency and conservation of Alu-initiated TSS in lncRNA in humans vs. mouse

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target networks, likely those influencing tf transcription
# (coordinated by Haru, WP6) knockdown of lncRNAs, measuring influence of lncRNAs, probing transcriptional network perturbations

==Structure features/subclassification of lncRNAs==
The intention here is to provide a comprehensive classification of lncRNAs based on structural features with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, positioning relative to other genome markers, etc.) However, quite a bit of this was performed in a recent paper by Cabili so we will have to see if there is scope for something new in FANTOM5.

# (Martin Frith & CBRC) structure of lncRNA with overlap with short RNA

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
# (Leonard,Alka) Rhett syndrome and cis-chain

==miRNA promoters==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) idefinition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Current best targets from Emily and Leonard sent to the OSC (Max and Al).
** Max and Al--> discussion with WP6.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome
** Lukasz/Nicolas (?) perform listed tasks
*** listed tasks are performed again on the set of predicted cis-acting and trans-acting lncRNAs, looking for differences

==General functional classification of lncRNAs==
* Nicolas cis-acting classification
** Leonard annotation of formal "Chainome"
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
**** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two
* Yulia Alu-S role in trans-acting lncRNAs

==Motif enrichment in promoter regions of lncRNAs==
* Boris motif enrichment
* Michiel MARA

==lncRNA conservation in matching mouse primary cells==
* ? defines determinants of lncRNA conservation
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
** ? conservation in promoter region vs. remaining sequence
* Leonard defines chain conservation
** Nicolas looks at genome-wide conservation of chains

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* CRBC general structural features of identified classes of lncRNAs
* take list of lncRNAs with overlapping short RNAs from above
** CRBC identification of "precursor" structure from RNA-seq and short RNA
** CRBC secondary structure predictions of lncRNAs in short RNA regions
*** CRBC integration of the two above

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation

==lncRNA and human disease overlap==
* Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* Leonard and Alka pursue Rhett story

FANTOM5 RNA-seq

2011-11-02T03:04:43Z

Burrough:

Noncoding RNA central page

2011-11-01T09:02:18Z

Burrough: /* ZENBU configuration */

Noncoding RNA central page

2011-11-01T08:57:11Z

Burrough: /* ZENBU configuration */

Noncoding RNA central page

2011-11-01T08:56:48Z

Burrough: /* ZENBU configuration */

Noncoding RNA central page

2011-11-01T08:44:39Z

Burrough: /* ZENBU configuration */

Noncoding RNA central page

2011-11-01T08:44:17Z

Burrough: /* ZENBU configuration */

Noncoding RNA central page

2011-11-01T08:30:04Z

Burrough: /* ZENBU configuration */

Noncoding RNA central page

2011-11-01T08:29:40Z

Burrough: /* ZENBU configuration */

Noncoding RNA central page

2011-11-01T08:28:07Z

Burrough: /* ZENBU configuration */

Long noncoding RNA main paper

2011-10-31T09:03:29Z

Burrough:

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see this page. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives=
This paper aims to capture the complete breadth and diversity of long noncoding RNAs (lncRNAs) while leveraging the unique qualities of FANTOM5 to understand their cellular restriction and evolutionary impact on the human genome. For the purpose of this paper, it is important to note that our definition of lncRNAs is more broader than others and includes bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE support. In addition, this paper will use genome organization and context to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

=Tasks for the paper=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Kouyou meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks will end up as satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard) Final tweaks to the FANTOM5 lncRNAome
## (Leonard) Inclusion of latest lncRNAs from the Cabili paper (?)
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks associating with lncRNAome from the final filtered and normalized clustering values
# (Lukasz) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and in different tissues (made available on the wiki to sample providers)
## (Lukasz) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz) Time course expression
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)

==General functional classification of lncRNAs==
Here we are interested in isolating lncRNAs likely to be acting in "cis" and making general functional predictions for individual lncRNAs based on co-expression. We are also interested in probing to what extent we can identify which lncRNAs may be involved in "trans" like regulation and which may primarily function as precursors for small RNA biogenesis.

Specific tasks:
# (Nicolas, Leonard) Preliminary classification of lncRNAs into likely cis- and trans- acting
## (Nicolas) sense-antisense co-expression at all lncRNA-mRNA sense-antisense pairs for latest data updates
## (Leonard) annotation of the above into a curated set representing the "Chainome"
## (Nicolas, Yulia) identification of potential trans-acting lncRNAs
# cis-acting lncRNA analysis (each analysis performed on both the complete set extracted by Nicolas and the chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains
## (Michiel) MARA analysis to see influence of cis-acting lncRNAs on transcriptional network (see motif enrichment section below)
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains
### similar to above, search for potential effects on expression of lncRNA and coding RNA in presence/absence of small RNA and its orientation
### (Eivind, Helena, Max, Martin, CRBC (see structure section below)) ncRNA serving as possible small RNA precursors
# trans-acting lncRNA analysis
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results
## (Yulia) direct/inverse co-expression patterns of lncRNAs with known-gene mRNAs with Alu-S in 3'UTRs (based on Gong and Maquat 2011 Nature paper)

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
# (Laurens) annotation of set of novel lncRNAs

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Comparisons of motif enrichment (difference in cis- vs. trans- ?)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome to identify possible candidates important to the transcriptional network

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse and human under the assumption that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken.

Specific tasks:
# (?) conservation frequency of human-specific lncRNAs in matching mouse primary cells
## (?) relative conservation of cis- and trans- acting
# (?) analysis of sequence conservation; promoter regions vs. the length of the transcript.
# (Leonard talks to Nicolas) conservation of "chainome"
# (Yulia for global analysis, Leonard for annotation) frequency and conservation of Alu-initiated TSS in lncRNA in humans vs. mouse

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target networks, likely those influencing tf transcription
# (coordinated by Haru, WP6) knockdown of lncRNAs, measuring influence of lncRNAs, probing transcriptional network perturbations

==Structure features/subclassification of lncRNAs==
The intention here is to provide a comprehensive classification of lncRNAs based on structural features with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, positioning relative to other genome markers, etc.) However, quite a bit of this was performed in a recent paper by Cabili so we will have to see if there is scope for something new in FANTOM5.

# (Martin Frith & CBRC) structure of lncRNA with overlap with short RNA

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
# (Leonard,Alka) Rhett syndrome and cis-chain

==miRNA promoters==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) idefinition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Current best targets from Emily and Leonard sent to the OSC (Max and Al).
** Max and Al--> discussion with WP6.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome
** Lukasz/Nicolas (?) perform listed tasks
*** listed tasks are performed again on the set of predicted cis-acting and trans-acting lncRNAs, looking for differences

==General functional classification of lncRNAs==
* Nicolas cis-acting classification
** Leonard annotation of formal "Chainome"
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
**** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two
* Yulia Alu-S role in trans-acting lncRNAs

==Motif enrichment in promoter regions of lncRNAs==
* Boris motif enrichment
* Michiel MARA

==lncRNA conservation in matching mouse primary cells==
* ? defines determinants of lncRNA conservation
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
** ? conservation in promoter region vs. remaining sequence
* Leonard defines chain conservation
** Nicolas looks at genome-wide conservation of chains

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* CRBC general structural features of identified classes of lncRNAs
* take list of lncRNAs with overlapping short RNAs from above
** CRBC identification of "precursor" structure from RNA-seq and short RNA
** CRBC secondary structure predictions of lncRNAs in short RNA regions
*** CRBC integration of the two above

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation

==lncRNA and human disease overlap==
* Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* Leonard and Alka pursue Rhett story

Long noncoding RNA main paper

2011-10-31T08:19:39Z

Burrough:

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see this page. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives=
This paper aims to capture the complete breadth and diversity of long noncoding RNAs (lncRNAs) while leveraging the unique qualities of FANTOM5 to understand their cellular restriction and evolutionary impact on the human genome. For the purpose of this paper, it is important to note that our definition of lncRNAs is more broader than others and includes bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE support. In addition, this paper will use genome organization and context to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

=Tasks for the paper=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Kouyou meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks can and will be made into satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard) Final tweaks to the FANTOM5 lncRNAome
## (Leonard) Inclusion of latest lncRNAs from the Cabili paper (?)
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks associating with lncRNAome from the final filtered and normalized clustering values
# (Lukasz) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and in different tissues (made available on the wiki to sample providers)
## (Lukasz) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz) Time course expression
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)

==General functional classification of lncRNAs==
Here we are interested in defining relative percentages of lncRNAs likely to be acting in "cis" or "trans" and making general functional predictions for individual lncRNAs based on co-expression.

Specific tasks:
# (Nicolas, Leonard) Preliminary classification of lncRNAs into likely cis- and trans- acting
## (Nicolas) construction of "cis-acting" lncRNA chains
## (Leonard) annotation of the above into a curated set representing the "Chainome"
## (Nicolas) subtraction of above yields set of potential trans-acting lncRNAs
# cis-acting lncRNA analysis (each analysis performed on both the complete set extracted by Nicolas and the chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains
### similar to above, search for potential effects on expression of lncRNA and coding RNA in presence/absence of small RNA and its orientation
# trans-acting lncRNA analysis
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Comparisons of motif enrichment (difference in cis- vs. trans- ?)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse and human under the assumption that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken.

Specific tasks:
# (?) conservation frequency of human-specific lncRNAs in matching mouse primary cells
## (?) relative conservation of cis- and trans- acting
# (?) analysis of sequence conservation; promoter regions vs. the length of the transcript.
# (Leonard talks to Nicolas) conservation of "chainome"
# (Yulia for global analysis, Leonard for annotation) frequency and conservation of Alu-initiated TSS in lncRNA in humans vs. mouse

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target networks
# (coordinated by Haru, WP6) knockdown of lncRNAs, measuring influence of lncRNAs

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
# (Laurens) annotation of set of novel lncRNAs

==Structure features/subclassification of lncRNAs==
The intention here is to provide a comprehensive classification of lncRNAs based on structural features with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, positioning relative to other genome markers, etc.) However, quite a bit of this was performed in a recent paper by Cabili so we will have to see if there is scope for something new in FANTOM5.

# (Martin Frith & colleagues?) structure of lncRNA with overlap to short RNA

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest. Analysis of eRNA is being headed up by Robin Andersson (robin@binf.ku.dk).

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
# (Leonard,Alka) Rhett syndrome and cis-chain

==miRNA promoters==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) idefinition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Current best targets from Emily and Leonard sent to the OSC (Max and Al).
** Max and Al--> discussion with WP6.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome
** Lukasz/Nicolas (?) perform listed tasks
*** listed tasks are performed again on the set of predicted cis-acting and trans-acting lncRNAs, looking for differences

==General functional classification of lncRNAs==
* Nicolas cis/trans differentiation
** Leonard annotation of formal "Chainome"
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
**** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two

==Motif enrichment in promoter regions of lncRNAs==
* Boris motif enrichment
* Michiel MARA

==lncRNA conservation in matching mouse primary cells==
* ? defines determinants of lncRNA conservation
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
** ? conservation in promoter region vs. remaining sequence
* Leonard defines chain conservation
** Nicolas looks at genome-wide conservation of chains

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* take list of lncRNAs with overlapping short RNAs from above
** ? identification of "precursor" structure from RNA-seq and short RNA
** ? secondary structure predictions of lncRNAs in short RNA regions
*** ? integration of the two above

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation

==lncRNA and human disease overlap==
* Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* Leonard and Alka pursue Rhett story

Long noncoding RNA main paper

2011-10-31T08:18:07Z

Burrough:

Welcome to the FANTOM5 long noncoding RNA (lncRNA) main paper page. This page will be used to list tasks and discuss ongoing analyses for the paper. For information on ncRNA data resources, see this page. Please keep in mind that this paper has already been the subject of extensive discussion in many forums and we need to move quickly on this paper. While we are always interested in exciting new analyses, if you have something new to introduce/propose please do so with the intention of personally carrying out the analysis.

=Paper objectives=
This paper aims to capture the complete breadth and diversity of long noncoding RNAs (lncRNAs) while leveraging the unique qualities of FANTOM5 to understand their cellular restriction and evolutionary impact on the human genome. For the purpose of this paper, it is important to note that our definition of lncRNAs is more broader than others and includes bidirectional/nested/cis-antisense lncRNAs and unspliced single-exon lncRNA genes with hCAGE support. In addition, this paper will use genome organization and context to probe functional properties and provide a comprehensive classification scheme for lncRNAs.

=Tasks for the paper=
If you are interested in assisting with a task below, please add your name before the task in parantheses. Names have already been added for people expressing interest or currently involved in tasks as discussed at the FANTOM5 Kouyou meeting. There are still tasks with no one assigned, if you are interested please put your name down. Conceivably, some of these tasks can and will be made into satellite papers which will be referred to by the main paper but we are including them here at present.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
Leonard Lipovich's lab has undertaken and completed the Herculean task of assembling and annotating the set of non-redundant, known lncRNAs and supplemented this with the set provided by Gencode. Preliminary viewing of the analysis in ZENBU suggests many lncRNAs are tissue-specific; this is an important point of order for the FANTOM5 data and this main paper.

Specific tasks:
# (Leonard) Final tweaks to the FANTOM5 lncRNAome
## (Leonard) Inclusion of latest lncRNAs from the Cabili paper (?)
# (WP4, Nicolas, Leonard) Obtain the list of hCAGE promoter peaks associating with lncRNAome from the final filtered and normalized clustering values
# (Lukasz) Primary-cell specific expression
## (Lukasz) Top-expressed lncRNAs in the total dataset and in different tissues (made available on the wiki to sample providers)
## (Lukasz) Identification of "cell-type" specific lncRNAs (made available on the wiki to sample providers)
# (Lukasz) Time course expression
## (Lukasz) Significant differences in lncRNA expression across time points across all time courses
## (Lukasz) lncRNA expression shared across multiple time courses
# (Lukasz) Analysis of lncRNAs (done in comparison with analysis of coding RNA--i.e. main promoterome paper analysis)
## (Lukasz) House-keeping vs tissue-specific lncRNAs (vs. coding RNAs)
## (Lukasz) Clustering of primary cells/tissues with respect to their lncRNA expression profiles
## (Lukasz) PCA and multidimensional scaling to find tissues with most lncRNA expression differences / similarity (vs. coding RNA)
# (Lukasz) All of the above tasks can be repeated to look for differences in cis- and trans-acting lncRNAs (see below)

==General functional classification of lncRNAs==
Here we are interested in defining relative percentages of lncRNAs likely to be acting in "cis" or "trans" and making general functional predictions for individual lncRNAs based on co-expression.

Specific tasks:
# (Nicolas, Leonard) Preliminary classification of lncRNAs into likely cis- and trans- acting
## (Nicolas) construction of "cis-acting" lncRNA chains
## (Leonard) annotation of the above into a curated set representing the "Chainome"
## (Nicolas) subtraction of above yields set of potential trans-acting lncRNAs
# cis-acting lncRNA analysis (each analysis performed on both the complete set extracted by Nicolas and the chainome curated by Leonard's lab)
## (Timo, Robin, Nicolas) linking lncRNA expression to groups of locally-connected genes
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs and effects of lncRNAs on chains
## (Eivind, Helena, Max) overlaying small RNA information with ncRNA found in chains
### similar to above, search for potential effects on expression of lncRNA and coding RNA in presence/absence of small RNA and its orientation
# trans-acting lncRNA analysis
## (Eivind, Finn, Tom, Nicolas) co-expression analysis to inform function of individual lncRNAs
## (Nicolas) reverse, window-based homology analysis of trans-acting lncRNAs to determine potential sites of activity on the genome
### overlay this analysis with co-expression results

==Motif enrichment in promoter regions of lncRNAs==
# (Boris Jankovic) Comparisons of motif enrichment (difference in cis- vs. trans- ?)
# Location/orientation of binding motifs within promoters
# (Michiel) MARA analysis on lncRNAome

==lncRNA conservation in matching mouse primary cells==
Anayzing the presence/absence of lncRNA peaks in mouse and human under the assumption that lncRNAs play a specific role in shaping the human/primate transcriptome. Many of these analyses could also be extended to aortic smooth muscle cells in rat, dog, and chicken.

Specific tasks:
# (?) conservation frequency of human-specific lncRNAs in matching mouse primary cells
## (?) relative conservation of cis- and trans- acting
# (?) analysis of sequence conservation; promoter regions vs. the length of the transcript.
# (Leonard talks to Nicolas) conservation of "chainome"
# (Yulia for global analysis, Leonard for annotation) frequency and conservation of Alu-initiated TSS in lncRNA in humans vs. mouse

==Network validation==
Probing lncRNA function through perturbation in identified networks.

Specific tasks:
# (Emily, Leonard) selection of candidate target networks
# (coordinated by Haru, WP6) knockdown of lncRNAs, measuring influence of lncRNAs

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq page for [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq details].
# (Max) collection of usable public RNA-seq data
# (Max) integration with FANTOM5 RNA-seq
# (Nicolas, Max) CAGE-scan integration
# (Laurens) annotation of set of novel lncRNAs

==Structure features/subclassification of lncRNAs==
The intention here is to provide a comprehensive classification of lncRNAs based on structural features with the help of RNA-seq and short RNA data (e.g. splicing architecture, evidence of processed intermediates, translational potential, positioning relative to other genome markers, etc.) However, quite a bit of this was performed in a recent paper by Cabili so we will have to see if there is scope for something new in FANTOM5.

# (Martin Frith & colleagues?) structure of lncRNA with overlap to short RNA

==eRNA analysis==
eRNA (enhancer RNA) is a class of lncRNA of particular interest. Analysis of eRNA is being headed up by Robin Andersson ([robin@binf.ku.dk]).

Specific tasks:
# (Robin) identification/classification, percent lncRNAs that are eRNAs, along with rationale
# basic statistics (e.g. length distribution, etc.)
# cell specificity
# exploring relationship between eRNA and associated promoters interactions
## expression correlation
## mutual information approach
## intersection with publicly available spatial genomic organization data
#(Miura-san, Robin, Nicolas) validation of eRNA interaction with promoter regions by intersect with existing HiC (?) data and/or more targeted validations

==lncRNA and human disease overlap==
# (Kenny, Peter, Juha) overlaying GWAS data with lncRNA
## cis-/trans-enrichment, cell-specificity of affected lncRNAs, etc...
# (Leonard,Alka) Rhett syndrome and cis-chain

==miRNA promoters==
Satellite paper based on Eivind and Kawaji-san's work
# (Eivind/Kawaji-san) idefinition of miRNA promoters based on DROSHA-KD, small RNA-seq and upstream hCAGE peaks

=Timeline/order of analyses=
Instead of wasting time assigning a bunch of meaningless dates to each task, I'll work out some of the dependencies which gives an idea of the prioritization. Then we'll follow up with groups assigned to the tasks as soon as they can be accomplished. The lists below are structured to imply dependency (indented tasks follow non-indented tasks...)

This is all dependent on finalization and normalization of the Kawaji-san promoterome clusters; however, everything listed below can begin using available data. After RNA-seq is used to confirm novel lncRNAs from FANTOM5, we may need to rerun a selected portion of the analyses on this set and possibly on the integrated set.

==Network validation==
Given the time this will require, we should get moving with what we have currently.
* Current best targets from Emily and Leonard sent to the OSC (Max and Al).
** Max and Al--> discussion with WP6.

==Annotation/analysis of the non-redundant lncRNAome across FANTOM5 dataset==
* Leonard submits final tweaks to the lncRNAome
** Lukasz/Nicolas (?) perform listed tasks
*** listed tasks are performed again on the set of predicted cis-acting and trans-acting lncRNAs, looking for differences

==General functional classification of lncRNAs==
* Nicolas cis/trans differentiation
** Leonard annotation of formal "Chainome"
*** Timo, Robin, Nicolas establishing locally-connected genes with lncRNA chains
*** Eivind, Finn, Tom, Nicolas co-expression analysis on chains and complete set
**** Eivind, Helena, Max overlaying small RNA information on chains and effects of small RNA on expression
* Eivind, Finn, Tom, Nicolas co-expression analysis on trans-acting lncRNAs
* Nicolas identifying complete space of physical interaction for trans-acting lncRNAs
** Nicolas overlaying the above two

==Motif enrichment in promoter regions of lncRNAs==
* Boris motif enrichment
* Michiel MARA

==lncRNA conservation in matching mouse primary cells==
* ? defines determinants of lncRNA conservation
** ? basic statistics on human/mouse conservation (possibly dependent on cis-/trans- classification)
** ? conservation in promoter region vs. remaining sequence
* Leonard defines chain conservation
** Nicolas looks at genome-wide conservation of chains

==Identification of novel lncRNAs using RNA-seq/CAGE-scan==
see RNA-seq [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/FANTOM5_RNA-seq page].
* Laurens will receive the complete set of novel lncRNAs for further annotation

==Structure features/subclassification of lncRNAs==
* take list of lncRNAs with overlapping short RNAs from above
** ? identification of "precursor" structure from RNA-seq and short RNA
** ? secondary structure predictions of lncRNAs in short RNA regions
*** ? integration of the two above

==eRNA analysis==
* Robin percentage of lncRNAs that are eRNAs and rationale for choosing this
* Robin basic statistics/cell specificity
* Robin eRNA and affected promoter analysis
** Robin/others computational validation with public datasets
* Miura-san wet lab validation

==lncRNA and human disease overlap==
* Kenny/others GWAS overlap with lncRNAome set
** accompanying analysis
* Leonard and Alka pursue Rhett story