Re: [Geuvadis_rna_analysis] analysis group TC Nov 15 at 2pm

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 &lt;Tuuli.Lappalainen(a)unige.ch <mailto: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 <tel:%2B49%20692%20573%20804%2041> Netherlands +31 108 920 271 <tel:%2B31%20108%20920%20271> Spain +34 931 816 661 <tel:%2B34%20931%20816%20661> Sweden +46 840 309 949 <tel:%2B46%20840%20309%20949> Switzerland +41 58 262 07 22 <tel:%2B41%2058%20262%2007%2022> United Kingdom +44 203 370 57 19 <tel:%2B44%20203%20370%2057%2019> United States +1 646 381 08 89 <tel:%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)22-3795550 <tel:%2B41-%280%2922-3795550> tuuli.lappalainen(a)unige.ch <mailto:tuuli.lappalainen@unige.ch> _______________________________________________ Geuvadis_rna_analysis mailing list Geuvadis_rna_analysis(a)lists.crg.es <mailto:Geuvadis_rna_analysis@lists.crg.es> http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis _______________________________________________ Geuvadis_rna_analysis mailing list Geuvadis_rna_analysis(a)lists.crg.es http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis