Wiki - User contributions [en]

Satellite citation

2014-02-24T14:08:13Z

Yulia:

* Jessica Severin, Marina Lizio, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Yoshihide Hayashizaki, the FANTOM consortium, Nicolas Bertin, and Alistair RR Forrest. “Interactive visualization and analysis of large-scale NGS data-sets using ZENBU”. Nature Biotechnology, http://dx.doi.org/10.1038/nbt.2840 (2013)

* Hideya Kawaji, Marina Lizio, Masayoshi Itoh, Mutsumi Kanamori-Katayama, Ai Kaiho, Hiromi Nishiyori-Sueki, Jay W. Shin, Miki Kojima-Ishiyama, Mitsuoki Kawano, Mitsuyoshi Murata, Noriko Ninomiya-Fukuda, Sachi Ishikawa-Kato, Sayaka Nagao-Sato, Shohei Noma, Yoshihide Hayashizaki, Alistair R.R. Forrest, Piero Carninci, and the FANTOM consortium. "Comparison of CAGE and RNA-seq transcriptome profiling using a clonally amplified and single molecule next generation sequencing". Genome Research, doi: 10.1101/gr.156232.113

* Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki, Evgenia Ntini, Erik Arner,, Eivind Valen,, Kang Li, Lucia Schwarzfischer, Dagmar Glatz, Johanna Raithel, Berit Lilje, Nicolas Rapin,, Frederik Otzen Bagger,, Mette Jørgensen, Peter Refsing Andersen, Nicolas Bertin,, Owen Rackham,, A. Maxwell Burroughs,, J. Kenneth Baillie, Yuri Ishizu,, Yuri Shimizu, Erina Furuhata, Shiori Maeda,, Yutaka Negishi,, Christopher J. Mungall, Terrence F. Meehan, Timo Lassmann, Masayoshi Itoh,,, Hideya Kawaji,, Naoto Kondo,, Jun Kawai,, Andreas Lennartsson, Carsten O. Daub,Peter Heutink, David A. Hume, Torben Heick Jensen, Harukazu Suzuki, Yoshihide Hayashizaki, Ferenc Müller, the FANTOM consortium, Alistair R.R. Forrest Piero Carninci Michael Rehli Albin Sandelin. "An atlas of active enhancers across human cell types and tissues" Nature doi:10.1038/nature12787

* Yulia A Medvedeva, Abdullah M Khamis, Ivan V Kulakovskiy, Wail Ba-Alawi, Md Shariful I Bhuyan, Hideya Kawaji, Timo Lassmann, Matthias Harbers, Alistair RR Forrest, Vladimir B Bajic and The FANTOM consortium, BMC Genomics 2013,15:119 doi:10.1186/1471-2164-15-119

* Regarding to the public version of "resource browser", please refer it as SSTAR ( http://fantom.gsc.riken.jp/5/sstar/ )

Satellite citation

2014-02-24T14:06:54Z

Yulia:

* Jessica Severin, Marina Lizio, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Yoshihide Hayashizaki, the FANTOM consortium, Nicolas Bertin, and Alistair RR Forrest. “Interactive visualization and analysis of large-scale NGS data-sets using ZENBU”. Nature Biotechnology, http://dx.doi.org/10.1038/nbt.2840 (2013)

* Hideya Kawaji, Marina Lizio, Masayoshi Itoh, Mutsumi Kanamori-Katayama, Ai Kaiho, Hiromi Nishiyori-Sueki, Jay W. Shin, Miki Kojima-Ishiyama, Mitsuoki Kawano, Mitsuyoshi Murata, Noriko Ninomiya-Fukuda, Sachi Ishikawa-Kato, Sayaka Nagao-Sato, Shohei Noma, Yoshihide Hayashizaki, Alistair R.R. Forrest, Piero Carninci, and the FANTOM consortium. "Comparison of CAGE and RNA-seq transcriptome profiling using a clonally amplified and single molecule next generation sequencing". Genome Research, doi: 10.1101/gr.156232.113

* Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki, Evgenia Ntini, Erik Arner,, Eivind Valen,, Kang Li, Lucia Schwarzfischer, Dagmar Glatz, Johanna Raithel, Berit Lilje, Nicolas Rapin,, Frederik Otzen Bagger,, Mette Jørgensen, Peter Refsing Andersen, Nicolas Bertin,, Owen Rackham,, A. Maxwell Burroughs,, J. Kenneth Baillie, Yuri Ishizu,, Yuri Shimizu, Erina Furuhata, Shiori Maeda,, Yutaka Negishi,, Christopher J. Mungall, Terrence F. Meehan, Timo Lassmann, Masayoshi Itoh,,, Hideya Kawaji,, Naoto Kondo,, Jun Kawai,, Andreas Lennartsson, Carsten O. Daub,Peter Heutink, David A. Hume, Torben Heick Jensen, Harukazu Suzuki, Yoshihide Hayashizaki, Ferenc Müller, the FANTOM consortium, Alistair R.R. Forrest Piero Carninci Michael Rehli Albin Sandelin. "An atlas of active enhancers across human cell types and tissues" Nature doi:10.1038/nature12787

* Yulia A Medvedeva, Abdullah M Khamis, Ivan V Kulakovskiy, Wail Ba-Alawi, Md Shariful I Bhuyan, Hideya Kawaji, Timo Lassmann, Matthias Harbers, Alistair RR Forrest, Vladimir B Bajic and The FANTOM consortium, BMC Genomics 2013,15:119

* Regarding to the public version of "resource browser", please refer it as SSTAR ( http://fantom.gsc.riken.jp/5/sstar/ )

File:Medvedeva et al accepted.zip

2013-11-28T11:32:44Z

Yulia: uploaded a new version of "File:Medvedeva et al accepted.zip"

File:Effect of cytosine methylation on transcription factor binding sites and regulation of transcription.doc

2013-11-28T11:19:15Z

Yulia: uploaded a new version of "File:Effect of cytosine methylation on transcription factor binding sites and regulation of transcription.doc"

2011-03-03T06:34:15Z

Yulia:

'''Task1: Sample acquisition/provision: '''Committed names: Al Forrest, Peter Klinken, Peter Heutink, Claudio Schneider, Kim Summers, Terry Meehan Output requirements/formats: Sample list - text to Al ASAP Milestones:       1. List of missing cellular states on wiki – March 10       2. Potential sources for missing states – March 10       3. Acceptance of last snapshots for phase 1 – March 31

 

'''Task2: Sample Annotation: '''Committed names: Terry Meehan, Win Hide, Tom Freeman, Al Forrest + sample providers Output requirements/formats: Cell ontology mapping, Tissue ontology mapping   ''Tom’s suggested Sample Annotation      1. UniqueID: Riken tracking number      2. Unique_sample_name: Adult_liver.r1 , Tcell_HPC-induced_10h (preferably short, informed by Cell_Ontology)      3. Species: Hs., Mm., etc.      4. Sample_Class: Adult_tissue (AT.), Foetal_tissue (FT.), Primary_cell (PC.), Cell_culture (CC.), Time_course (TC-PC.), (TC-CC) etc.      5. Developmental stage: Adult, Foetal      6. Pathology: Normal, disease      7. Tissue: Liver, brain, heart etc      8. Cell_Ontology (maybe more than one level, to be used in primary sample ordering): Mesenchymal etc, etc      9. Cell_type: CO approved name e.g. Monocyte, Smooth_muscle, Intestinal_epithelium etc.     10. Pertubation: LPS, HPC     11. Time: 0, 1h, 2h, 3h etc     12. Replicate: r1, r2, r3     13. Collection_method: FACS_sorting etc. with short description     14. Collection_method_reference: Pubmed_ID, web_address, protocol     15. Source: Roslin_Institute     16. Primary_contact: Joe_Bloggs     17. Email: joe.bloggs@roslin.ed.ac.uk     18. Tel: 0044 131 123 4567     19. Unique Donor ID''

Milestones:      1. Annotation of Data freeze 1 samples (cell, tissue – minimum to compare replicates)      2. Cell ontology – completion by March 15?      3. Tissue ontology – March 15

 

'''Task3: Mapping: '''Committed names: Timo Lassmann, Geoff Faulkner Output requirements/formats:      BAM      CTSS Milestones:      1. Rescuing assessment (March 5)      2. Decision (March 7)      3. Genome version agreement – comment on pseudoautosomal regions      4. Mapping of Data freeze 1 (GENAS??)

 

'''Task4: Tag clustering: '''Committed names: Piero Carninci, Cesare Furlanello, Piotr Balwierz, Martin Taylor, Martin Frith, Kawaji-san, Boris Lenhard, Albin Sandelin - clustering. David Hume, Ben Brown, Al Forrest - assessment Output requirements/formats:      1. Clusters defined as regions on a genome with strand, start, stop, peak and build(Bed?)      2. Intersect of the defined regions as an expression matrix/table across all samples (ie. intersect of clusters with expression in all libraries)      3. Possibly.. intersected CTSS file of same regions to allow study of independent peak regulation      4. Peak rec '' Tom’s suggestion      Data Matrix Annotation      To be provided by Riken as raw counts (.raw) and tags per million (.tpm) but ultimately data may be normalised by other methods (.xxx)      1. UniqueID: Gene Level (MGD, HGNC ID), Transcript or promoter level (ABC1.1, ABC1.2 etc), ncRNA (Leonard’s ID)      2. Class: Gene_promoter, ncRNA_promoter, other      3. Chromosomal_location: e.g. alignment range, promoter peak      4. Chromosome: Chr1      5. Associated_seqs: refseq, ensembl_gene/transcript, ncRNA_ref      6. Other_associations: KEGG, GO etc''

Milestones:     1. Agreement on format and training/tuning/assessment data and metrics (March 5)     2. Competitive tracks available – March 25     3. Assessment – April 5     4. Run over paper 1 data freeze – mid April

 

'''Task5: State enriched(expression weighted) motif predictions (ab-initio and known): '''Committed names:Vlad Bajic, Michiel de Hoon, Boris Lenhard, Kenneth Baiulie, Timo Lassmann, Piotr Balwierz, Yulia Medvedeva Output requirements/formats: Milestones:      1. Ranked list of motifs enriched in each state for release 010      2. Bed file(or similar) with actual predictions for release 010      3. As above on FREEZE 1

 

'''Task5: [[Tag Cluster Annotation]]: '''Committed names: Piero Carninci, Laurens Wilming, Timo Lassmann, Richard Baldarelli, Juha Kere, Leonard Lipovich(long ncRNA promoters, sense-antisense pair promoters, bidirectional promoters), Boris Lenhard(enhancers), Alison Meynert, Yulia Medvedeva (CpG islands, DNA methylation, Repeats) Output requirements/formats: Milestones:      1. Agreement on annotations to use (now?) (I will supply the global human lncRNAome and sense-antisense coordinates for the annotation. - LL)      2. Annotation of release 009 clusters using agreed strategy – available ASAP      3. Annotation of data freeze 1 (ASAP after the clusters are provided)

 

'''Task6: Cross species promoter mapping: '''Committed names: Martin Taylor, Colin Semple, Vlad Bajic, Peter Heutink, Max Burroughs, Soichi Ogishima, Leonard Lipovich (if we are doing non-conserved promoters) Output requirements/formats: 

''  Martins Taylor's suggested format''

''     species1_tag_cluster_ID      species1_genome_assembly_ID      species1_chrom      species1_refPos      species1_strand      species2_tag_cluster_ID      species2_genome_assembly_ID      species2_chrom      species2_refPos      species2_strand      projection_method (a list of rule sets whose criteria were met*)      projection_distance (a measure of confidence in the projection)      projection_result (e.g. species1_rescue, species2_rescue....)''

''     *e.g. identical projected modal tag position, quantile overlap of      projected tag cluster distributions, cluster coordinate overlap.''

Milestones:      1. Prediction/mapping of human promoters using mouse data (April 15)      2. Validation on the matched 10-30 human-mouse pairs (ie predict with mouse and check with actual human data). Assessment of strategy.      3. Prediction of human counterpart promoters for the rare mouse cells that we have collected (eg. intestinal stem cells, inner ear hair cells etc.).      4. Do we need a preliminary count of nonconserved human promoters (those absent from the other 4 F5 species)? (LL)     

 

'''Task7: Expression visualization (gene level AND TSScluster level): '''Committed names: Tom Freeman,Kenneth Baillie, Carsten Daub, Win Hide, Boris Lenhard, Albin Sandelin  Output requirements/formats: potential figures for displaying relationship of samples based on expression clustering Milestones:      1. Gene level information humanx3(tissue, cell line, primary cells) -> Biolayout webstart      2. Distance matrix, genes and pathways that separate each state - Win Hide

 

'''Task8: Promoter level expression analysis (differentially expressed genes/markers/transcription factors/ncRNAs): '''Committed names: Piero Carninci, Al Forrest, Albin Sandelin, Vlad Bajic, Yulia Medvedeva, Hideya Kawaji, Ben Brown, Tom Freeman, Harukazu Suzuki, Colin Semple, David Human, Cesare Furlanello, Kenneth Bailie and Jess Mar, Timothy Ravasi, Leonard Lipovich Output requirements/formats: Milestones: 1. Agreement on metric for specificity/enrichment – entropy Ravasi March 5 2. Ranked list of most specific TFs for each state 3. Ranked list of ncRNAs specific for each state (incl. curated lncRNAs that define specific steady states -LL) 4. Ranked list of all genes specific for each state

 

'''Task9: Expression data mining: '''Committed names: Carlo, Tim Output requirements/formats: Milestones:

1. Explore the data set using maximum curvilinearity methods and see if it helps classify the layers

Boosting? SVMs?

 

'''Task10: Motif activity and TF expression integration (including deorphanization): '''Committed names: Vlad Bajic, Michiel de Hoon, Piotr Balwierz, Yulia Medvedeva, Matthias Harbers, Al Forrest Output requirements/formats: Milestones: 1. Expanding Motifs 2. Core predicted set 3. Attempt at integrating list of sample enriched TFs and sample enriched motifs. 4. Prioritized orphan associations for validation

 

'''Task10: Sanity check: '''Committed names: Al Forrest, Piero Carninci Output requirements/formats: Milestones: 1. Assessment of strategy above 2. OK or repeat from step XYZ

 '''Task11: Data dissemination and nomenclature: '''Committed names: Win Hide, David Hume, Piero Carninci, Richard Baldarelli, Vlad Bajic, Tom Freeman, Yoshihide Hayashizaki, John Quackenbush, Laurens, Terry Meehan, Hideya Kawaji, Timo Lassmann, Albin Sandelin Output requirements/formats:      ‘Promoter’ – dissemination      ‘expression’ – dissemination      ‘cell/sample’ – dissemination? Milestones:      1. Agreement on strategy      2. Agreement on formats      3. Agreement on third party data repositories (especially UCSC and Ensembl)      4. Core promoters with accessions and link to our data nomenclature

 

'''Task12: ChipSeq Validation: '''Committed names: RIKEN OSC, Tim Ravasi, Al Forrest, Matthias Harbers, WP9 Output requirements/formats: Milestones:      1. Target selection – considering cell type, predictions, chip grade antibody, impact      2. Assessment of targets      3. Motif finding      4. Public chip-seq data

 

'''Task13: Public data integration: '''Committed names: Vlad, David, Yulia, Louise, Thomas, Terry, Matthias 

Milestones:

     1. Extract public Chip-seq data

     2. Extract public mouse KO

     3. Extract edges from literature mining (vlad)

     4. Extract in-situ mapping from Allen brain atlas, eurexpress, emage

     5. Extract localization information from human protein atlas 

 

'''Task14: KDCAGE Validation: '''Committed names: RIKEN OSC, WP9 (intersection of chip-seq known and ) Output requirements/formats: Milestones:      1. Target selection – considering cell type, predictions, impact      2. Assessment of targets      3. Motif finding

 '''Task15: In-situ validation: (likely very late in project) '''Committed names: Juha? Peter H? Silivia, Output requirements/formats: Milestones:    1. Target selection    2. In-situ on a small set of human samples    3. Likely very late in the project '''Task16: Paper4 - Cross species network conservation: '''Committed names: Al Forrest, Martin Taylor, Peter Heutink, Michiel de Hoon, Mamoon Rashid, Colin Semple, Vlad Bajic, Max Burroughs, Soichi Ogishima, Leonard Lipovich Output requirements/formats: Milestones:      1. Gene level ortholog pairs (CDS matching)      2. TSS cluster level ortholog pairs (genome matching)      3. Ortholog expression correlations (use expression data from above group, and ortholog mappings from 1 and 2)      4. State specific motif enrichment (conservation independent)      5. Tf state specific expression      6. siRNA KD of SMC specific TFs in multiple species      7. Potential chip-seq      8. Availability of Macaque samples? Aortic SMC, hepatocytes, Bone marrow MSCs      9. Macrophages across all species? Peripheral blood (PBMCs)      10. Integration of cis-networks (bidirectional promoters; TF to lncRNA; antisense lncRNA to sense mRNA gene) with existing networks -LL      11. Examples of specific non-conserved networks -LL

Tag Cluster Annotation

2011-03-03T06:29:50Z

Yulia: /* Committed names */

==Committed names==
* Piero Carninci
* Laurens Wilming
* Timo Lassmann
* Richard Baldarelli
* Juha Kere
* Leonard Lipovich(long ncRNA promoters, sense-antisense pair promoters, bidirectional promoters, global human lncRNAome and sense-antisense coordinates)
* Boris Lenhard(enhancers)
* [[User:ameynert|Alison Meynert]] (Ensembl gene models)
* Sarah Djebali
* Yulia Medvedeva (CpG islands, DNA methylation, Repeats)

==Annotations & assignments==

'''NB: we will need to be careful about 0-based and 1-based coordinates'''

Given the majority of people in FANTOM5 seem to be UCSC focused, propose we use 0-based UCSC format with 'chr' prefix. Any Ensembl or other 1-based annotations will need to be adjusted in the output and a note added to the flat file headers/README.

==Output requirements/formats==

===Proposal - flat file format===

[http://fantom.gsc.riken.jp/4/download/Tables/doc/ OSCtable] format tab-delimited file, separate files for each species, could also be separate files per annotation class, but should be able to mash together all files for a species into one without re-formatting.

Here is an initial sketch of a possible flat-file format (scroll right to see it all):

<pre>
##
## Contact name = Ann Otator
## Contact e-mail = ann.otator@institute
## Description = General annotations (or could be just e.g. Ensembl gene models, lncRNAs, enhancers)
## Species = Homo sapiens
## NCBI taxon id = 9606
## Release = FANTOM5 UPDATE_009
##
Tag_cluster_id Library_id Annotation_class Annotation_type Annotation_id Distance Chr Tag_cluster_pos Tag_cluster_strand Annotation_start Annotation_end Annotation_strand
TSC000001 CNhs11772 CORE_PROMOTER ENSEMBL_TRANSCRIPT ENST00000000001 -30 chr1 1234153 + 1234183 1238888 +
TSC000002 . 3_PRIME_UTR UCSC_TRANSCRIPT GENE1 . chr2 1234124 + 1234124 1289193 +
TSC000003 . CORE_PROMOTER LONG_NC_RNA LEONARD01 -2 chr3 4848484 - 4848400 4848482 -
TSC000004 CNhs11334 LONG_RANGE_REGULATION VISTA_ENHANCER VISTA001 . chr4 3893493 + 3893400 3893499 -
TSC000005 . EXTENDED_PROMOTER ENSEMBL_TRANSCRIPT ENST00000000002 -503 chr5 3485928 + 3482000 3486431 -
</pre>

If the library id is given, the tag cluster is associated with that specific library; otherwise, it is associated with the aggregate of all libraries. It is possible that some annotations will not be required on a per-library basis.

Some types of annotation (e.g. core promoter, extended promoter) we will want to include the distance from the tag cluster reference position to the annotation position (e.g. annotated protein-coding gene TSS). For other types (e.g. 3' UTR, exonic), it's enough to know that the tag cluster reference position overlaps that annotation, and the distance can be unspecified.

===Proposal - MySQL database schema===

Is this something that people would find useful? Here's a very de-normalized schema - another option is to have one table per species and just follow the flat-file format.

<pre>
CREATE TABLE library (

library_id VARCHAR(9) NOT NULL,
species VARCHAR(40) NOT NULL,
taxon_id INT(10) UNSIGNED NOT NULL,
source ENUM('primary cell', 'cell line', 'tissue', 'timecourse', 'quality control') NOT NULL,
description VARCHAR(100) NOT NULL,

PRIMARY KEY (library_id)

);

CREATE TABLE annotation (

annotation_id INT(10) UNSIGNED NOT NULL,
taxon_id INT(10) UNSIGNED NOT NULL,
class VARCHAR(40) NOT NULL,
source VARCHAR(40) NOT NULL,
type VARCHAR(40) NOT NULL,
external_id VARCHAR(40) NOT NULL,
chr VARCHAR(40) NOT NULL,
pos VARCHAR(40) NOT NULL,

PRIMARY KEY (annotation_id),
KEY annotation_idx (class, source, type, external_id),
KEY location_idx (chr, pos)

);

CREATE TABLE tag_cluster (

library_id VARCHAR(9) NOT NULL,
tag_cluster_id VARCHAR(40) NOT NULL,
chr VARCHAR(40) NOT NULL,
pos INT(10) UNSIGNED NOT NULL,

PRIMARY KEY (tag_cluster_id)
KEY location_idx (chr, pos)

);

CREATE TABLE tag_cluster_annotation (

annotation_id INT(10) UNSIGNED NOT NULL,
tag_cluster_id VARCHAR(40) NOT NULL,

KEY annotation_idx (annotation_id),
KEY tag_cluster_idx (tag_cluster_id)
);
</pre>

==Milestones==
# Agreement on annotations to use ([[Media:Annotation_ncRNA_and_promoters-discussion_group_F5.pdf|Working group notes from Piero]])
#*Set out annotation list and any definitions (e.g. core promoter vs. extended promoter) on this wiki page
#*Assignment of annotation types to participants
#*Agreement on output format - ASAP
# Annotation of release 009 clusters using agreed strategy
#*Are we waiting on the results of the tag cluster competition or is there a test set of clusters that we can start working on?
# Annotation of data freeze 1 - ASAP after freeze

Satellite papers

2011-03-01T16:12:47Z

Yulia: /* Methylation effect on TFBS and expression (Yulia) */

= Instructions =

Below you can find the list of satellite paper proposals collected in the February meeting. Please add the following information to each of the proposals

*Check the title
*provide brief outline of the proposal
*add/remove your name in case you are interested to work on this satellite paper

Proposal for satellites papers 2/25/2011 Purpose: list up potential satellites; avoid redundancies, make better papers Figure out potential titles to discuss how to negotiate with specific journals.

Add a set of sentences (mini abstract) on the wiki and write an abstract

= Bioinformatics analysis methods =

== Normalization and clustering issues ==

*Outline: bla
*Group members: Tom Freeman

== Modulation of gene expression (Jess Mar) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Expanding transcriptional reg. networks (Vlad) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Tag clusterin in helicos CAGE (Cesare) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Computation methods for networks comparisons]] (cesare) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Tool to make the promoter subsets at will (do not ask us datasets!) (Albin) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Delve tag mapping paper (Timo L) ==

*Outline: Methods paper on Delve: a probabilistic read mapper.
*Group members: Timo Lassmann, Carsten Daub

== Classification of CAGE peaks (Timo L) ==

*Outline: Deeply sequenced CAGE libraries capture signals on many non-promoter regions. The purpose of this paper is to describe a strategy to separate TSS from non-TSS CAGE peaks (see: [[media:CAGE_classification.pdf]]). Preliminary work suggest that further sub-classicifation of promoters based on the shape of the CAGE signal is possible (see: [[media:Brood_october_2010.pdf]]).
*Group members: Timo Lassmann, Ben Brown, Colin Semple

== Peak finder-noise elimination contest paper (all runners) ==

*Outline: bla
*Group members: xxx, yyy, zzz

= Genomics-broad scale analysis =

*Outline: bla
*Group members: xxx, yyy, zzz

== Alternative TSS in cancer relevant to biomarkers (Win Hide) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Impact of alternative promoters on biology of genes (Albin) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== How much do we need to sequence? Complexity of the transcriptome (Albin) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Revised analysis of zinc finger proteins (Tim Ravasi, David Hume) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Identification of distal regulation elements: role of enhancers in differentiation (Carsten, Boris, Ana P, Jose, YH) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== miRNA promoters (Hideya K, Eivind Al, ) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== CAGE tags on Pigs: Gain and loss of promoters (David Hume) [satellite of the pig genome] ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Regulatory transcription outside canonical promoters (Boris) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Transcription initiation in embryo development (Boris) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Promoters with multiple TSS configuration-multiple ways to use the same promoters (Boris, Kawaji) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Link Fantom 5 to genetic datasets (Peter Heutink; Juha K) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Methylation effect on TFBS and expression (Yulia) ==

*Outline: It's commonly accepted that DNA methylation of a promoter repress transcription of this gene in normal tissues. Recently, a class of actively expressed genes having relatively methylated promoters has been discovered. The purpose of this research is to explore the idea that DNA methylation effects CG-rich TFBS, preventing TF from binding to DNA, and therefore represses transcription.

*Group members: Yulia Medvedeva

== Comparison of different types/feature of promoters and genome features to study specific differences (Yulia) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Multiple genomics analysis on multiple datasets (Haru) Extension of the validation? ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Prediction of cell transformation states (Win Hide) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Convergent evolution of retrotransposon promoters (Geoff) ==

*Outline: Following the model for the anti-apoptosis gene NAIP (Romanish et al., PLoS Genetics, 2007), we will start by screening the mouse and human genomes for instances where two different retrotransposons occupy the same or similar location in protein-coding genes (e.g. an Alu in human, a B2 in mouse). If this happens frequently enough to be interesting, we will overlay the F5 data onto the "convergent" retrotransposons to see how many are transcribed, what role they may have in regulation (e.g. Lunyak et al., Science, 2007) and if the events are more common for some pathways than others (e.g. in embryogenesis or brain development). 
*Group members: Geoff, Piero 

== Alternative TSS and alternative splicing (Nicolas) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Chimaeric RNA and 3D structure (if it works) (Nicolas) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Annotation of genes involved in biochemical, metabolic processes and signature for processes-for instance signature for tumors – expression based GO terms (Tom Freeman) (Richard Baldarelli, Jackson and GO groups) (David Hume) ==

*Outline: bla
*Group members: xxx, yyy, zzz

 

= Blood group: fill in the holes, more discussion =

== Granulopoiesis analysis (Andreas Lenn.) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Cellular restriction of epigenomic regulation Erik A. + Andreas Lenn. ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Eritropoiesis (Peter K) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== HSC (Sugiyama san) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Macrophages (DH) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Subpopulations T cells and monocytes (Michael R) ==

*Outline: bla
*Group members: xxx, yyy, zzz

= Brain groups 4 papers Other priority areas in brain: discuss other brain and diseases (YH) =

== Evolution gene expression in vertebrates Martin + Peter Heutink ==

*Outline: Study the evolution of gene expression combining insights from each of the following:
** Gene/transcript level changes in expression (and estimating it's constraint/diversification).
** TSS/promoter turnover: orthologous genes using non-orthologous promoters, or changes in promoter-preference for one cell type between species.
** Sequence evolution of core promoters and distant regulatory blocks correlated with changes in gene expression.
* Focus of the paper on the well matched cells between ((Human, (Macaque?)),(Mouse, Rat),Dog),Chicken) for which we have hCAGE data. (Cell types: Hepatocytes, Aortic smooth muscle cells, mesenchymal stem cells).
*Group members: Martin Taylor, Peter Heutink, Alison Meynert
*Details: [[Evolution in gene expression]].

== Transcriptional constrains seq evolution [Martin+Michiel talk] ==

*Outline: [Michiel:] Network analysis across organisms & evolution of regulatory networks, in particular of developmental networks. Are there any subnetworks particularly conserved between organisms? What does this tell us about the functional importance and relevance of specific subnetworks? Do we see any recurring patterns in the network (Uri Alon-type feed-forward loops)? What are the conservation patterns and rates of divergence of transcription factors and specific regulatory relations? Do we see turnover of TFBSs, or do we see conservation of TFBSs in alignments? This can be applied specifically to brain, or more generally to all CAGE samples. TFBS prediction in Neanderthal compared to Homo sapiens would be really cool.
*Group members: Martin, Michiel, Peter Heutink
*Martin's and Michiel's idea for this paper may overlap or may be complementary to each other; we need to discuss this. This may end up as two satellite papers or one integrated one.

== Tfbs turnover in liver (integrate with ChIP seq) Martin ==

*Outline: Integration of cross-species ChIP-seq data in liver with proximal CAGE tag cluster responses in the same species. Data on liver ChIP-seq for the transcription factors HNF1A and CEBPA in human/mouse/dog/(chicken) Schmidt et al, Science 2010 has been obtained. The questions we can address with this study are:
** Are conserved binding sites more likely than non-conserved sites to elicit a local, hepatocyte specific ranscriptional response? (Use CEBPA non-expressing cells to generate a background model of proximal transcriptional responses). This could be used to estimate "functional turnover" as opposed to the "binding turnover" as reported by Duncan Odom.
** Does hepatocyte specific expression (around binding sites) segregate through species lineages with the experimentally defined binding site?
** If there is apparent turn-over of binding sites, is the pattern of local responsive transcription conserved?
** Do we see conservation of hepatocyte specific transcriptional responses even in the absence of binding site conservation?
*Group members: Martin Taylor, Alison Meynert

== Disease paper (brain): human post mortem, … comparison healthy-disease Peter Heutink + Gustincich group ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Rett syndrome and visual cortex Alka ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Genomic architecture in 3 genes involved in Rett syndrome Alka ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Genomic architecture of neurodegenerative disease (Gustincich talk P.H., etc.) ==

*Outline: bla
*Group members: xxx, yyy, zzz

= Others =

== [[Olfactory receptors]] ==

*Outline: Promoters of [[Olfactory receptors]] (ORs) are still poorly documented. We have an unpublished promoter list for mouse, and CAGE libraries from human olfactory mucosa will be made. We will identify the promoters of the human ORs and analyse their structure. Many ORs have [[Alternative Promoters|alternative promoters]] and this is a potential example for the promotorome paper. Human-specific OR promoters might be found. There is evidence of expression of the ORs outside the mouse and human olfactory mucosa, and this satellite paper will report this. Experiments to find a ligand and propose a function may be carried out. More information on the page: [[Olfactory receptors]].
*Group members: [[User:Plessy|Charles Plessy]], Giovanni Pascarella, Stefano Gustincich and others, but I am too shy to add their name without asking.

== Cell-Cell communicatome (Al forrest) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Drugable cells: drug targets (Al Forrest) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Definition of stem or precursors relationship (Claudio Schneider) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Gene regulation in cells of connective tissues (Vlad, Kim) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Transdifferentiation and network rewiring (Haru; WP6 + others) POTENTIAL main paper for later stage ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Network in cancer (Rama, win’s group) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Regulatory network in cell lineage tree (Carsten wp5) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Determination of conserved CAGE (Vlad) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Promoting human uniqueness: human-specific promoters of regulatory lncRNA genes drive cis- and trans-regulation. (LL) ==

*More information at: [[Regulatory lncRNAs: 'promoting' human uniqueness]]
*Outline: TBD
*Group members: Leonard Lipovich, Yulia Medvedeva (inviting you to join - please confirm), Vlad Bajic (inviting you to join - please confirm), Jess Mar (inviting you to join - please confirm), and I am also too shy to name (or invite) potential others. Please email me or the F5 list, or please just add yourselves to this page, if you would like to work on this.
* Anticipated ABSTRACT (Big Picture of what we will likely see, with actual numbers coming later; XXX, YYY etc are placeholders for the actual numbers).
In FANTOM3, we learned that complex loci -- sense-antisense pairs, bidirectional promoters, and gene chains -- are prevalent in mammalian genomes. These complex loci often contain long non-coding RNA (lncRNA) genes which have the potential to cis-regulate protein-coding genes, but whose sequences and genomic structures are often not conserved between human and mouse (Katayama et al 2005; Engstrom et al 2006). The specific contribution of non-conserved sequences to regulation at complex loci has remained obscure. To quantify and characterize the functional significance of non-conserved lncRNA regulation, we have used the FANTOM5 human CAGE Promoterome to catalog: XXXXXX Transcription Start Sites (TSS) in single-copy human genomic sequences unalignable to mouse, rat, dog/pig(?), and chicken; and the FANTOM5 human CAGEscan data to define XXXXX additional human TSS-s inside primate-specific Alu repeats (all collectively defined as "human-specific TSS-s"). We computed the intersection of these human-specific TSSs with: XXXX nonredundant lncRNA genes from our cDNA-supported lncRNA catalog and from other groups; XXXX human bidirectional promoters of lncRNA-mRNA gene pairs; and ~2800 lncRNA-mRNA sense-antisense pairs identified by our sense-antisense discovery pipeline. XXXXX human-specific TSS-s belonged to standalone lncRNA genes, YYYYY to lncRNA genes in lncRNA-mRNA sense-antisense and bidirectional-promoter pairs, and ZZZZZ to lncRNA genes in chains; therefore, {YYYYY+ZZZZZ} (##% of total) human-specific TSS-s are associated with lncRNA genes that may cis-regulate protein-coding genes. Here, we apply the FANTOM5 human tissue and primary cell culture resource to describe human spatiotemporal lncRNA-mRNA co-expression in gene pairs and chains, finding that XXX co-expressed lncRNA-mRNA pairs depend on human-specific lncRNA TSS-s. Comparative manual annotation of mouse transcriptome data reveals that XXX of the orthologous mouse mRNAs lack any evidence of adjacent or antisense lncRNA transcription, suggesting that the corresponding CAGE-supported human lncRNA TSS-s are indeed human-specific. We infer XXX specific transcriptional cis-regulatory networks consisting of known transcription factors, human-specific lncRNA promoters, lncRNAs, and mRNAs regulated by the lncRNAs. Protein-coding genes in these cis-networks are preferentially expressed in specific {WHICH?} tissues and are enriched in specific {WHICH?} functions {INSERT RESULTS HERE: BRAIN? SYNAPTIC PLASTICITY? RELEVANCE TO HIGHER-ORDER BEHAVIORS??}, defining a unique functional space occupied by the non-conserved human lncRNA-mRNA cis-co-regulome. Cell-culture-based reverse-genetic interrogation of {SELECTED} lncRNAs with human-specific TSS-s, by RNAi and overexpression, confirms both the cis-regulatory potential of lncRNAs with human-specific promoters to modulate their genomic neighbor genes and the trans-regulatory effects of such modulation on the rest of the protein-coding transcriptome (NOTE - this is only possible if OSC can help us with validations). These results indicate that, while the genomics community primarily pursues the function of multispecies conserved sequences, interspecies gene structure differences caused by non-conserved lncRNA promoters are functional in evolutionary lineage-specific regulation.
== Using single direction promoter ti eliminate noise (Yulia) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Specific transcript (Human) regulation and what are nover TF in human (Haru) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Identification of TFBS by de novo methods (Vlad; Boris) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Predicted homotypic clusters and motif prediction (Yulia) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Identification fo features of primates specific promoters (?; together with LL) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Regulation specificity of cells and tissues (Vlad’ s group) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Host pathogen infection relationship; influenza virus, Mycobacteria, Salomonella (Arnab) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Searching for viruses, cryptic viruses (Arnab, mamoon, al, nico) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Deorphanizing transcription factors (Vlad) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Variation in small RNA population and variation in siRNA machinery (Max) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Cellular restriction of terminal ligases in ubiquitin system (Max) ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Papers of individual cells time courses ==

*Outline: bla
*Group members: xxx, yyy, zzz

== [[Extend rat gene models with CAGEscan]] ==

*Outline: Rat gene models sometimes lack a proper 5′ UTR. CAGEscan data has been produced using the same RNA (10009-101B8) as the reference FANTOM5 Helicos CAGE library CNhs10612. This experimental data can be used to propose an update of the rat gene models.
*Group members: [[User:Plessy|Charles Plessy]], Albin Sandelin, other people, please list yourself.

== [[Novel metrics for promoter activity profiles]] ==

== [[Pathway Fingerprinting]] ==

= Issues: negotiation with sample providers =

== Encouraged to write paper, but larger stronger papers is perhaps better? ==

*Outline: bla
*Group members: xxx, yyy, zzz

== Talk with collaborator before the datasets is published ==

*Outline: bla
*Group members: xxx, yyy, zzz

[[Category:Satellite_paper]]