geuvadis_rna_analysis October 2012

geuvadis_rna_analysis@lists.crg.es

8 participants
19 discussions

by Mar Gonzàlez-Porta

Hi everyone, Please find below the links to two new pages on the wiki describing the results of my analyses + pointing to slides/supplementary files: http://sanabre.net/geuvadis/index.php/Ubiquity_vs_specificity_of_gene_and_i… http://sanabre.net/geuvadis/index.php/Differential_isoform_usage Cheers, Mar

12 years

[Geuvadis_rna_analysis] analysis updates

by Tuuli Lappalainen

Hello, First a question: Who would like to present on Thursday's analysis group call? Next week we should discuss splicing QTLs (with results from Jean and myself), but this week's slot is free. Then a couple of analysis updates: - I've done some analysis on miRNA-mRNA interactions; namely on whether miRNA-cis-eQTLs show increased trans-signal to the targets of these miRNAs. The answer is maybe yes - the signal is small but significant. See http://sanabre.net/geuvadis/index.php/MiRNA-mRNA_interaction . - I've updated some normalizations of quantifications - I let some of you know about these already during the weekend, but for FYI for eneryone. Details in http://sanabre.net/geuvadis/index.php/Basic_methodology#Normalization_of_th… . These are quantifications done jointly on the 462 samples by PEER, and then transforming the residuals to standard normal (*norm* in the filename). There are files for miRNAs (full and seed-pooled), exons, splice junctions, introns, and transcripts in the directories below: /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/mirna/quantification_tables /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/quantification/exon/ /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/quantification/splice_junction-intron /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/quantification/splice_junction-intron /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/quantification/transcript 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

12 years

[Geuvadis_rna_analysis] Wiki on some splicing features and sQTL

by Jean Monlong

Hi all, Just to let you know I put some results on the wiki about simple splicing features(http://sanabre.net/geuvadis/index.php/Qualitative_and_quantitative…, some alternative splicing comparison (http://sanabre.net/geuvadis/index.php/Alternative_splicing_analysis) and splicing QTL results (http://sanabre.net/geuvadis/index.php/Splicing_QTL_discovery_using_transcri…). Among the interesting results, again "cell division" popped up of the GO analysis when looking at genes with different splicing features and splicing QTL results look good with enrichment in exons, some good share across population and interesting GWAS hits nearby. I'll put the results file on the ftp tomorrow, I'll be happy to present/comment the analysis anytime(except next call because I'll be on the plane to Barcelona). Feedback/ideas are very welcome, Thanks, Jean

12 years

[Geuvadis_rna_analysis] main paper

by Tuuli Lappalainen

Hello, In order to keep things rolling for the main paper, I've put together a list of action items for all of us, as well as an early draft of supplemental figures and tables. The main figure draft has been updated a bit as well. There are plenty of placeholders for us to fill, and let's discuss these on the call tomorrow - these are definitely open for discussion. I'd also like to emphasize that now when we're finalizing the analysis and I'm trying my best to put it all together, we should have subgroup or one-on-one calls if you don't understand what I'm asking from you, or if it seems that I'm misunderstanding your analysis. best, Tuuli The action items are here (as well as in the attached document): Everyone - Text for the supplement: methods, results, and conclusions of your analysis. - Good-quality figures (see doc for details) - Deadline: October 20 Tuuli - finish splicing QTLs - plenty of downstream analysis of QTLs - rare variant mapping - Loss-of-function ASE NMD stats - ASAS / ASE sharing analysis - finish some QC analyses - ...a zillion other things Micha - Coordinate documentation of mRNA mapping and transcript quantification - Coordinate splicing paper - some plot(s) of splicing variation (coefficient of variation? Annotated/novel junctions vs population freq?) - Final figures: - gene discovery plot that works in smaller space - splice score distributions - allele frequency distributions for splicing score categories (DAF from annotations in vcf) Marc - miRNA-mRNA correlation analysis Jean - quantitative analysis of population differences (e.g. GBR-CEU looks visually the same as GBR-YRI, but is this really true numerically? Compare all population pairs) - prettier figures of transcript quantification stats - prettier figures of quantitative vs qualitative variation Mar & Pedro - Prepare a Venn-diagram of splice/expression differentiated genes and plot some examples Liliana - quantitative values of fusion events for QTL analysis - prettier frequency and distance plots Manny - Stop-gained NMD compensation - Splice effect modeling with Micha's scores - NMD prediction - Coordinate LoF paper Peter - coordinate QC paper Irina - results of repeat analysis - quantitative values for QTL analysis? Maarten - miRNA-mRNA correlation analysis Matthias - prettier plots that illustrate soft splicing variation: - phenomenon in general: the lineplot that shows the distances from the major spliceoform - population variation in an analogous way to Jean's analysis Daniela - results of n-TAR analysis - quantitative values of n-TARs for QTL analysis Thomas - results of RNA editing analysis - quantitative values of editing for QTL analysis Monkol & Daniel - annotation statistics (variants in each category) -- 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

12 years

[Geuvadis_rna_analysis] REMINDER: GEUVADIS survey DEADLINE tomorrow

by Gabrielle Anne Bertier

This is to remind you that the deadline for the survey is tomorrow. Here are the results so far per country: Denmark 1 Estonia 1 France 2 Germany 4 Ireland 1 Slovenia 1 Spain 8 Sweden 6 Switzerland 7 the Netherlands 5 Turkey 4 We still have no response from many European countries, which lowers the value of our survey. Please get in touch with me if you know specific people who have not filled in the survey and can do so quickly. You'll find the names of the institutes who have answered below, Kind regards, Gabrielle Dept. Medical Sciences, Molecular Medicine national centre for medical genetics The EStonian Genome Center of University of Tartu Diagnostikcentrum, Clinical Pathology and Clinical Genetics University of Lausanne CHUV Uppsala University; SNP&SEQ Technology platform + Uppsala Genome Center University Hospital Copenhagen Institute of Medical Genetics at the University of Zurich Kantonsspital Olten Division of Human Genetics Leiden University Medical Center Center for Human Genetics and Laboratory Medicine Institut Central des Hopitaux Valaisans-RSV Humangenetics İstanbul University Institute of Experimental Medicine Max Planck Institute for Molecular Genetics UMC Utrecht Leiden University Medical Center TUBITAK, MAM, Genetic Engineering and Biotechnology Institute VUMC Lund University Diabetes Centre Science For Life Laboratory Department of Medical genetics & Inserm U 910 Helmholtz Zentrum Zentrum München Hôpital Timone Enfants et faculté de Médecine Center for Genomic Regulation INGEMM Fundacion Investigación Clínico de Valencia-INCLIVA Instituto de Salud Carlos III Uppsala University. Immunology, Genetics and Pathology / SciLifeLab Hospital Universitario Ramon y Cajal Hospital de Terrassa Complexo Hospitalario Universitario de Santiago Clinical institute of medical genetics Ljubljana Maastricht UMC+, Department of Clinical Genetics Sabanci University Institute of Medical Genetics and Applied Genomics, University of Tuebingen Hospital San Pedro de Alcántara TUBITAK-BILGEM From: Gabrielle Anne Bertier Sent: 28 September, 2012 18:12 PM To: 'geuvadis_partners(a)lists.crg.es'; 'geuvadis_exome(a)lists.crg.es'; 'geuvadis_wpl(a)lists.crg.es'; 'geuvadis_rnaseq(a)lists.crg.es'; 'geuvadis_rna_analysis(a)lists.crg.es' Cc: Xavier Estivill; Michela Bertero; 'Bea Sobrino' Subject: IMPORTANT NOTICE: GEUVADIS survey DEADLINE EXTENDED Dear all, I remind you that we would highly appreciate if you could fill in, and distribute our survey on NGS to all your relevant colleagues. Note that we've extended the deadline to the 10th October 2012 Full survey link: https://qtrial.qualtrics.com/SE/?SID=SV_bHJDue550PwdFrv To describe the survey please use freely the following text: ------------------ THE GEUVADIS PROJECT - More information on our website: www.geuvadis.eu<file:///C:\Users\gbertier\Documents\GEUVADIS\Annual%20Meeting%202\www.geuvadis.eu> The latest high-throughput next-generation sequencing technologies allow investigators to sequence entire human genomes and transcriptomes at an affordable price and within a short time frame. An increasing number of research centers in Europe have access to these technologies, in-house or through regional, national and international infrastructures. Storing, disseminating and analysing the large amount of data produced generate major challenges. Tackling these challenges requires extensive exchange of data, information and knowledge between sequencing centers, bio-informatics networks, the medical research community and the industry at the European level. The GEUVADIS (Genetic EUropean VAriation in DISease) Consortium has four main aims: 1. Develop standards in quality control and assessment of sequence data 2. Develop models for sequencing data storage, access and exchange 3. Develop standards for the handling, analysis and interpretation of sequencing data from DNA (and RNA) 4. Develop guidelines on the handling of ethical, legal and social implications of phenotype prediction from sequence variation * PURPOSE OF SURVEY 1. Collect quantitative and qualitative information on the current status of DNA sequence production, storage, exchange and analysis in Europe. 2. Collect feedback from research/clinical centers on their main challenges and difficulties regarding the management of these large data-sets potentially containing important medical information 3. Collect information on local standardization efforts, and avoid duplication of efforts throughout Europe 4. Create a road-map/policy document outlining the necessary steps to take national standards to the European level * POTENTIAL PUBLICATION OF RESULTS 1. Results of this survey will be presented at an internal GEUVADIS workshop, on October 30-31st 2012. 2. We will disseminate the road-map to potential funders (private of public), including the European Commission and other possible national public funders. 3. We will submit an abstract to the Joint Conference of Human Genome Meeting 2013 and 21st International Congress of Genetics. * DEADLINE: 30.09.2012 --------------------- If you have any question or comment regarding the Annual Meeting, the workshop and/or the survey please don't hesitate to contact me. 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

12 years

[Geuvadis_rna_analysis] TC minutes

by Tuuli Lappalainen

Hello, Here are some badly belated minutes from last week's analysis group TC. The next call will be this Thursday, October 11 at 2pm CET. - There's a new conference call system of a shared screen and notes that we can use later if we want to - Maarten presented some early results from miRNA-mRNA correlations. The background null distribution looks good and unbiased, and hopefully refining the analysis a bit further will help us to get a significant signal out of this. - Micha presented a draft plot for the paper of how gene discoveries increase as a function of sequenced samples - After the main call we had a splicing subgroup call - different splicing measures and splice scores of variants seem to correlate nicely, there's plenty of data and analysis is going well, although there's plenty of things to do especially wrapping up the sQTLs. - The next call will have a splicing theme: Micha will present splice junction analyses, and if there's time Tuuli will present allele-specific alternative splicing. For those who are interested, I've already updated the wiki with ASAS methods analyses (http://sanabre.net/geuvadis/index.php/Allele_specific_alternative_splicing). 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

12 years

[Geuvadis_rna_analysis] presentation for today's TC

by P.A.C._t_Hoen＠lumc.nl

Dear all Please find attached a document describing an approach and initial results for miRNA:mRNA integration that Maarten van Iterson will discuss during today's TC Peter Dr. Peter A.C. 't Hoen Center for Human and Clinical Genetics Leiden University Medical Center Postal zone S4-P PO Box 9600 2300 RC Leiden The Netherlands phone: +31-71-5269421 fax: +31-71-5268285 e-mail: p.a.c.hoen(a)lumc.nl

12 years

[Geuvadis_rna_analysis] Geuvadis RNA analysis TC today - Details

by Gabrielle Anne Bertier

Dear all, This is a reminder of our TC today at 14:00 CET Here are the details of the call: Agenda Analysis updates Presentation from Leiden After the main call we'll continue with a subgroup to discuss splicing analyses; anyone interested is welcome to stay for that too. Dial-in Germany 08001013982 Netherlands 0107994092 Spain 900800678 Sweden 0752400458 Switzerland 0800705347 United Kingdom 08005285280 United States 3032489677 Access code: 3160100

12 years

[Geuvadis_rna_analysis] GEUVADIS RNAseq paper -- TC doodle

by Gabrielle Anne Bertier

Dear all, Please fill in the following doodle for the next GEUVADIS RNAseq TC on the project's publication: http://www.doodle.com/pdeyynfz3rnwvtaf?lt=2<http://www.doodle.com/pdeyynfz3rnwvtaf?lt=1> Preliminary agenda would be: - outlines of the main paper and the QC companion paper - practicalities of publication - other companion papers 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

12 years

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

geuvadis_rna_analysis October 2012