Hello all,
We had a teleconference today to discuss the feedback that we got from
Nature. The next call will be in one week, *Thursday 31st at 4pm CET. *
*A**ction item*s:
- Everyone: by next week's call, please think/discuss within your
group what kind of future companion projects you are working or are
planning to launch based on Geuvadis data/samples.
- all who have added content to the wiki: please go through the
material that you have there: delete outdated content, and if needed:
add material and reorganize. Some missing content is tolerable,
incorrect information is not.
A brief summary of today's discussion:
- Manolis and myself have sent Nature's editor Magdalena Skipper a
rebuttal letter to address the points raised by the reviewers, and the
plan is to discuss with her soon. Let's hope that she will give us the
chance to revise the paper after all - we think that there's a decent
chance.
- On the call there was discussion of some of the most important
questions that the reviewers raised and the potential improvements based
on that (regardless of whether we'll resubmit to Nature or to another
journal). Depending on what happens with Nature, I'll coordinate the
details of the revisions later with the respective people.
- Figure 1c raised questions but it's a pretty strong analysis
already. Include the splicing manuscript in the next submission will
show that we've worked on these questions in further depth
- data access: from the Geuvadis browser we'll provide downloads of
the full master files as well as regions. The Ensembl broswer where the
bams can be visualized doesn't have a slicing functionality and it's
well beyond our resources to start building that. Tuuli will provide
Natalja with a list of the final master files of quantifications etc.
that we'll want to share once the paper is out.
- Jean is doing some additional analysis to estimate how robust the
transcript variation statistics are to lowly expressed gene as well as
lowly expressed transcripts of highly expressed genes.
- In addition to transcript ratio QTLs, we could also do
polyadenylation QTLs - Pedro has quantified these already, and it might
add to the novelty of the paper and address the question of variation in
transcript structure.
- Regarding the robustness of the analysis, Peter had a good idea
of taking the old eQTLs from April (different mapper, normalization and
eQTL method, analysis by population) to show that the results are highly
overlapping (I believe and hope that they are). We could also e.g.
quantify 5 samples with Cufflinks and show that flux is similar but
better, or map to personalized genomes, but we need to think very
carefully how deep we want to get into these types of analyses and how
we'd interpret the results before we do anything. Regarding allelic
mapping bias, it should be enough if we just describe Tuuli's existing
analysis better in the paper.
- One of the reviewers suggested that dropping some of the analyses
might improve the paper. I'm not keen to do that, but we'll discuss this
with Magdalena and if she wants us to do that, that's what we'll do.
- Gabrielle created a visitor read-only access to the wiki so that
the reviewers can go and take a look.
So, now it's time to cross your fingers again and hope that our letter
convinces Magdalena to reconsider the rejection. We'll let you know when
have her decision.
best,
Tuuli
Tuuli Lappalainen, PhD
Department of Genetics, Stanford University School of Medicine , and
Department of Genetic Medicine and Development, University of Geneva
Email:tuuli.e.lappalainen@gmail.com /tlappala(a)stanford.edu
Tel: +1 415 351 9713
Bustamante lab
Department of Genetics
300 Pasteur Dr. Lane L301
Stanford, CA 94305-5120
USA
On /24/113 3:28 AM, Gabrielle Anne Bertier wrote:
Dear all,
Here are the details for the call:
*TODAY - Thursday 24th January at 16:00 CET*
SPAIN
900800678
GERMANY
08001013982
NETHERLANDS
08002658044
FRANCE
0800947739
UNITED KINGDOM
08005285280
UNITED STATES
8005369053
SWEDEN
0201400578
From Other countries
+34 917911859
Access code:
3160100
Thanks alot,
Kind regards,
Gabrielle
*/Gabrielle Bertier/*
/Scientific Project Manager
International and Scientific Affairs
CRG, Center for Genomic Regulation
Carrer Dr. Aiguader, 88/
/08003 Barcelona, España
/Tel: +34933160374
Mobile: +34639960656
email: gabrielle.bertier(a)crg.es <mailto:gabrielle.bertier@crg.es>
web:www.geuvadis.eu;
www.fliact.eu
*From:*geuvadis_rna_analysis-bounces@lists.crg.es
[mailto:geuvadis_rna_analysis-bounces@lists.crg.es] *On Behalf Of
*Tuuli Lappalainen
*Sent:* 22 January, 2013 8:37 AM
*To:* Manolis Dermitzakis; geuvadis_rna_analysis(a)lists.crg.es
*Subject:* [Geuvadis_rna_analysis] RNAseq paper
Dear all,
The Geuvadis RNAseq paper was rejected this morning. We've decided
with Manolis that we should make an appeal, and we have already been
in touch with Magdalena about this. We'll need to send her a response
letter in a couple of days (see the attachment with reviewer's
comments and a rough response draft). It ain't over til it's over.
Since we were going to have a call soon anyway, let's have a *TC on
Thursday the 24th at 4pm CET*. Before that, I'd be happy to hear your
*comments to the response letter (deadline: immediately)*. There's a
couple of bigger items to discuss, and specific questions to a few of
you - see below. There won't be a lot of new analysis to do if we're
given the chance to revise.
Questions:
- Do we drop non-essential analyses as #2 suggests? This would mean
RNA editing, maybe fusions and subtle splicing. I'm not keen to, but
if people think it would improve the overall quality of the paper...
- Should we restructure the supplement by topic instead of
methods/figures/tables? Need to ask Magdalena too.
- Andrew & Natalja: Can we add a data slicing and download function to
the browser (or a separate site linked from the browser)?
- Jean & Mar: How is the qualitative/quantitative analysis affected by
low-abundance transcripts? Will the results change if the threshold is
different?
- Jean, Mar, Pedro, Micha (and myself): #2 raises an important
question (really!): most of transcript variation is explained by
transcript ratio differences, but we find very few QTLs for this. Why
do you think this is? Is all that variation really just
random/environmental/epigenetic?
- Jean: #3 suspects that the 3% of transcriptome variation explained
by population could be just random - how do we respond to this?
- Manny: What could we do to add novelty value to NMD analysis?
- Gabrielle: Is it possible to make a read-only password for the wiki?
We could give one to the reviewers just so that they can see it.
best regards,
Tuuli
--
Tuuli Lappalainen, PhD
Department of Genetics, Stanford University School of Medicine , and
Department of Genetic Medicine and Development, University of Geneva
Email:tuuli.e.lappalainen@gmail.com <mailto:tuuli.e.lappalainen@gmail.com>
/tlappala(a)stanford.edu <mailto:tlappala@stanford.edu>
Tel: +1 415 351 9713
Bustamante lab
Department of Genetics
300 Pasteur Dr. Lane L301
Stanford, CA 94305-5120
USA
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