Small RNA paper page

HEY! welcome to the short RNA FANTOM paper page. This paper is being headed up by Helena Persson, Eiven Valen, Michiel de Hoon (?), and Max Burroughs. Anyone interested is free to join in, just shoot an email over to Max (burrough@gsc.riken.jp) with your ideas for analyses, contributions for the paper.

Overview

The strength of the FANTOM5 short RNA dataset is 1) overall scope of the samples (not the depth in any sample) and 2) matching hCAGE expression data.

Data

Contrary to what was said at the Kouyou meeting, we have ~300 total samples sequenced, not total number of primary cells. The ~300 number includes replicates. Here is the detailed breakdown:

Multiplication table

category	1	2	3
1	1	2	3
2	2	4	6
3	3	6	9
4	4	8	12
5	5	10	15

Brainstorming:

• novel miRNA prediction, tissue specific: Helena
• endo siRNA: Eiven/Helena?
• coding/noncoding overlapping short RNA and mechanistic implications?: Eiven
• cell-specific short RNA derived from known precursors: ?
• cell-specific novel short RNA populations. I suspect these two are quite related, "novel" populations will likely be derived from known precursors which are significantly differentially processed in certain cell lines. I think its better to look for the differential expression of all tags instead of looking specifically at known noncoding classes--max
• 'differential' post-transcriptional modifications: Max
• differential expression of tiRNAs and how this effects hCAGE expression across the panel

• one analysis we will need to do for the lncRNA paper is to overlay lnRNA-intersecting short RNA with to see if/how this influences the chains

Notes:

• I vote for RLE normalization. It performs slightly better than TMM or tpmm and its easy. see this page for details. I can play around and see if RLE performs better on all tags (with a cut-off) or on just miRNA loci. (Max)
• see if we can get some timecourses. this would give the paper another angle and Helena points out it would be useful to show important RNAs for wet-bench collaborators
• eventually it might be nice to account for the relatedness of samples; I'm thinking we can wait to see what the promoterome paper does and then adopt that but until then we just use some naive differential expression technique?
• defining 'clusters' for promoter-based RNAs/endo-siRNAs other novel populations could be a bit tricky
• might be nice to do expression comparisons between short RNAs and hCAGE peaks, could be an additional form of validation for novel
• Helena might be able to provide (limited) validation for novel miRNAs