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
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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