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
The ensuing link leads to a ZENBU configuration containing tracks with pooled hCAGE, pooled short RNA, and pooled FANTOM5 RNA-seq expression data. 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.
FANTOM5 paper pages
- long non-coding RNA paper centered on chains/networks of lncRNAs and coding RNAs
- FANTOM5 novel lncRNA search with RNA-seq (likely to be folded into the main paper above)
- 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 lncRNAome (Lipovich lab): Media:F5_human_lncRNAome(Jia&Lipovich_Gencode)BED.zip
- FANTOM5 sense/antisense pairing (Nicolas/Lipovich lab): Media:F5_human_sense-antisense_pairs_hg19.zip
- chains! (forthcoming)
- novel predicted lncRNA from FANTOM5 data (forthcoming)
- integrated Lipovich lncRNAome + novel lncRNA from FANTOM5 data (forthcoming)
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 selected for RNA-seq (forthcoming, target: Nov. 1)
- 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)
CAGE-scan
- links to currently-available raw data (69 samples)
- 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.
- 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
