15 Nov
2012
15 Nov
'12
5:54 a.m.
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
tuuli.lappalainen(a)unige.ch
15 Nov
15 Nov
12:35 p.m.
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
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
1:51 p.m.
Hello,
Here's the current outline of the main paper for discussion.
cheers,
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(a)unige.ch
On /15/1112 12:35 PM, Michael Sammeth wrote:
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 <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
18 Nov
18 Nov
11:25 a.m.
New subject: [Geuvadis_rna_analysis] analysis group TC Nov 15 at 2pm - minutes
Hello,
Here are (belated) minutes of last Thursday's TC. The next call will be
in November 22nd at 2pm CET.
- First, the most important point: The few remaining analysis results
and methods text need to be sent to Tuuli *without delay*. The deadline
was weeks ago, and now we can't wait any longer - I have already drafted
the main paper.
- We got very good feedback at the Geuvadis annual meeting in Santiago
de Compostela. A couple of important decisions regarding the RNAseq WP
were made:
- we decided to make a pre-publication data release of fastqs and
bams, so the files are now out there, esiset access is through
www.geuvadis.org. This was announced at the 1000 Genomes meeting,
advertised in San Francisco in general, and now also mentioned in the
1000G website. The data is under embargo until publication of the main
paper.
- we discussed the author list - the latest version for the main
paper can be seen under the data link. In addition to the ~60 named
authors, there will be a "the Geuvadis consortium" listed before the
PIs, and acknowledgements will include e.g. technicians. In the
companions and subsequent papers, the people involved in that particular
analyses should be named, and "the Geuvadis consortium" author will
contain all the authors of the main paper, indexed and visible to PubMed.
- people thought that making the wiki open to the public when the
paper comes out is a good idea
- there was discussion on future RNAseq experiments but no definite
decisions on this
- At the ASHG meeting in SF people were in general very interested and
impressed by our work. We discussed with editors of Nature and Science
and both were interested in the paper; our first target will be Nature
as discussed before. However, there is competition: a group from
Stanford will be submitting a major RNAseq paper in the end of November,
and while they don't have genome sequencing data and the analyses are
not too badly overlapping, we really need to hurry up now so that their
paper is not accepted before we submit.
- The main paper outline was discussed. Due to the competition
situation, we need to submit by December 15, which is doable if we work
hard. Tuuli has finished writing the first draft of the main paper text;
this will be sent around soon. As mentioned above, any pending analyses
need to be finished right now or they are very unlikely to make it to
the paper. We are putting together the Supplement now but still missing
methods text from 1-2 of you. Please send it to me without delay.
- We discussed the outline of the splicing paper. We should be able to
submit that at the same time with the main paper.
best regards,
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(a)unige.ch
On /15/1112 5:54 AM, Tuuli Lappalainen 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
tuuli.lappalainen(a)unige.ch
_______________________________________________
Geuvadis_rna_analysis mailing list
Geuvadis_rna_analysis(a)lists.crg.es
http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
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geuvadis_rna_analysis@lists.crg.es
3 comments
2 participants
participants (2)
-
Michael Sammeth -
Tuuli Lappalainen