Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans
Authors: Pouya Kheradpour
Dana R Valley
Michael T Moser
Carolyn Compton
Matthew Stephens
Angela Britton
Gen Li
Anuar Konkashbaev
Laura A Siminoff
Kenyon Erickson
Monkol Lek
Amanda Brown
Leslie H Sobin
Lucas D Ward
David S Deluca
Andrey A Shabalin
Jeffery P Struewing
Jialiang Yang
Yvonne Marcus
Timothy J Sullivan
Kimberly M Valentino
Quan Long
John Syron
Timothée Flutre
Yan Meng
Scott D Jewell
Mary Barcus
Karna L Robinson
Liqun Qi
Gary D Walters
Mark I McCarthy
Heather M Traino
Maghboeba Mosavel
Luan Lin
Cameron D Palmer
Bryan M Gillard
Barbara A Foster
Fred A Wright
Christopher Choi
Mehran Taherian
Susan Koester
Ki Sung Um
Kristin G Ardlie
Alexis Battle
Gary F Temple
John T Lonsdale
Rick Hasz
Tuuli Lappalainen
David Tabor
Daphne Koller
Ellen T Gelfand
Pushpa Hariharan
Harold Magazine
Nancy J Cox
Johnell Fleming
Pedro G Ferreira
Sara Mostafavi
Zhidong Tu
Ping Guan
Bin Zhang
Halit Ongen
Philip A Branton
Robin Burges
Simona Volpi
Jonathan K Pritchard
Jun Zhu
Jorge Tejada
Joanne P Demchok
Kimberly Ramsey
Roderic Guigó
Laura K Barker
Kenneth W Hambright
Daniel G MacArthur
Tõnu Esko
Anna M Smith
Eric R Gamazon
Chunrong Lu
Anita H Undale
Jakob M Goldmann
Greg E Korzeniewski
Latarsha J Carithers
Jimmie B Vaught
Susan Sullivan
Manuel A Rivas
John Seleski
Charles Shive
Manolis Kellis
Sherilyn J Sawyer
Ayellet V Segrè
Yi-Hui Zhou
Hae Kyung Im
Joel N Hirschhorn
Mark Miklos
Edmund Lo
Helen M Moore
Michael Sammeth
Saboor Shad
Nancy Roche
Gad Getz
Taylor R Young
Nicole C Lockhart
Bernadette Mestichelli
Chana A Rabiner
Deborah Colantuoni
Jason P Bridge
Ellen Karasik
Debra Bradbury
Jeffrey McLean
Roger Little
Michael Salvatore
Deborah C Mash
Marta Melé
GTEx Consortium
Jeffrey A Thomas
Ferran Reverter
Shenpei Wu
Tao Huang
Taru Tukiainen
Joy Boyer
Andrew B Nobel
Denee Tidwell
Julian B Maller
Wendy Winckler
Dan L Nicolae
Benjamin Iriarte
Jun Liu
Jean Monlong
Stephen A Buia
Emmanouil T Dermitzakis
Ivan Rusyn
Xiaoquan Wen
Daniel C Rohrer
Margaret Basile
Casandra A Trowbridge
Journal: Science (2015)
Discipline: Multidisciplinary
Keywords: genetic variation; complex human disease; quantitative traits; RNA sequencing data; tissues

Abstract:  Understanding the functional consequences of genetic variation, and how it affects complex human disease and quantitative traits, remains a critical challenge for biomedicine. We present an analysis of RNA sequencing data from 1641 samples across 43 tissues from 175 individuals, generated as part of the pilot phase of the Genotype-Tissue Expression (GTEx) project. We describe the landscape of gene expression across tissues, catalog thousands of tissue-specific and shared regulatory expression quantitative trait loci (eQTL) variants, describe complex network relationships, and identify signals from genome-wide association studies explained by eQTLs. These findings provide a systematic understanding of the cellular and biological consequences of human genetic variation and of the heterogeneity of such effects among a diverse set of human tissues. 

Retracted: No

PubPeer comments:
 In the figure S18, A-C and B-D panels seem to be rigorously identical, which I guess shouldn t be the case in regard of the nature of the analysis ![file] , 
 Good catch. This was a bug in my code, and none of us noticed that the panels were identical, nor alerted us before now. After digging through files and code from 2014, I produced a plot that shows the statistics for 16 and 30 reads - extracting the correct numbers for the coverage of 8 reads would have required more work, and it didn t seem very relevant at this stage. ![file] For anyone interested in more recent GTEx ASE data and statistics, I recommend the v8 ASE companion paper: https: genomebiology.biomedcentral.com articles 10.1186 s13059-020-02122-z ![file] ,