Tentative title:

Splicing Singularities and Population Polymorphisms of Human Transcriptomes

(1) transcriptome composition varies with gene expression

- although gene discovery does not saturate,

most genes of a certain tissue are expressed ubiquitously across individuals and populations

- population-determinant genes (specific from 1 population) show proliferant factors

age of cell line bias, pairwise distances and tree

- differentially expressed genes accumulate for cell surface factors

(2) transcriptome configuration changes by differential splicing (DS)

- most genes show little transcript variability

- most variable genes show enrichment for cell surface terms (?),

but no significant overlap with DE genes (!)

- alternative psi exons (splicing only)

(3) genetic polymorphisms that influence DS

- fraction of variants in splice site regions,

compare to subgenic localization of sQTLs

- classification of splice site variants in 5 distinct groups, characterization:

activating variants differ in allele frequencies, deteriorating vs. neutral/enhancing indicative of psi exons

(4) discovery of novel elements by RNAseq

- intron variants, number of donors/acceptors...weak are predominantly rare in population

- how many novel events, broken down by type, characterization

Bottom line

- the transcriptomes differ not markedly between individuals/populations

- but quantitative (gene expression level) and qualitative (splicing level) differences occur not (only) at random

On Thu, Nov 15, 2012 at 5:54 AM, Tuuli Lappalainen <Tuuli.Lappalainen@unige.ch> wrote:

Hello all,

We'll have an RNAseq analysis group TC today at 2pm CET. Apologies for the late notice.

I hope many of you can attend since it's been a while due to me traveling; there are a number of important things to discuss:

- updates from Santiago de Chile
- updates from ASHG
- outline, timeline and action items for the main paper
- outlines, timelines and action items for the companion papers
- analysis updates
- AOB

Call details:
Germany       +49 692 573 804 41
Netherlands       +31 108 920 271
Spain         +34 931 816 661
Sweden         +46 840 309 949
Switzerland       +41 58 262 07 22
United Kingdom         +44 203 370 57 19
United States       +1 646 381 08 89
Access code: 611683

best,
Tuuli

-- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen@unige.ch
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