Noncoding RNA central page

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 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:

1. CAGE-scan/RNA-seq transcripts could crash your browser at loci with a large amount of expression.
2. 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 F5 human lncRNAome BED file (n=19599) is now available. The corresponding F5 human lncRNAome Excel file, which contains LEGENDS and ANNOTATIONS that cannot be incorporated into the BED, will be updated soon.

1. As annotation (remember to select "bed_region" to obtain the full trancsript like complete structure)
2. As a single track in DEX (somewhat more convenient that selecting it as an "annotation")
3. Under this link, the latest lncRNAome dataset now replaces the previous ("F5_human_lncRNAome_28July2011") one.
4. 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 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 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 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 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

• 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