Here some update on the splicing companion outline:
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(a)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 <%2B49%20692%20573%20804%2041>
Netherlands +31 108 920 271
Spain +34 931 816 661
Sweden +46 840 309 949
Switzerland +41 58 262 07 22 <%2B41%2058%20262%2007%2022>
United Kingdom +44 203 370 57 19 <%2B44%20203%20370%2057%2019>
United States +1 646 381 08 89 <%2B1%20646%20381%2008%2089>
*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)22-3795550tuuli.lappalainen(a)unige.ch
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