Authors
Ashis Saha, Yungil Kim, Ariel DH Gewirtz, Brian Jo, Chuan Gao, Ian C McDowell, Barbara E Engelhardt, Alexis Battle, François Aguet, Kristin G Ardlie, Beryl B Cummings, Ellen T Gelfand, Gad Getz, Kane Hadley, Robert E Handsaker, Katherine H Huang, Seva Kashin, Konrad J Karczewski, Monkol Lek, Xiao Li, Daniel G MacArthur, Jared L Nedzel, Duyen T Nguyen, Michael S Noble, Ayellet V Segrè, Casandra A Trowbridge, Taru Tukiainen, Nathan S Abell, Brunilda Balliu, Ruth Barshir, Omer Basha, Gireesh K Bogu, Andrew Brown, Christopher D Brown, Stephane E Castel, Lin S Chen, Colby Chiang, Donald F Conrad, Nancy J Cox, Farhan N Damani, Joe R Davis, Olivier Delaneau, Emmanouil T Dermitzakis, Eleazar Eskin, Pedro G Ferreira, Laure Frésard, Eric R Gamazon, Diego Garrido-Martín, Genna Gliner, Michael J Gloudemans, Roderic Guigo, Ira M Hall, Buhm Han, Yuan He, Farhad Hormozdiari, Cedric Howald, Hae Kyung Im, Eun Yong Kang, Sarah Kim-Hellmuth, Tuuli Lappalainen, Gen Li, Xin Li, Boxiang Liu, Serghei Mangul, Mark I McCarthy, Pejman Mohammadi, Jean Monlong, Stephen B Montgomery, Manuel Muñoz-Aguirre, Anne W Ndungu, Dan L Nicolae, Andrew B Nobel, Meritxell Oliva, Halit Ongen, John J Palowitch, Nikolaos Panousis, Panagiotis Papasaikas, YoSon Park, Princy Parsana, Anthony J Payne, Christine B Peterson, Jie Quan, Ferran Reverter, Chiara Sabatti, Michael Sammeth, Alexandra J Scott, Andrey A Shabalin, Reza Sodaei, Matthew Stephens, Barbara E Stranger, Benjamin J Strober, Jae Hoon Sul, Emily K Tsang, Sarah Urbut, Martijn van de Bunt, Gao Wang, Xiaoquan Wen, Fred A Wright, Hualin S Xi, Esti Yeger-Lotem, Zachary Zappala, Judith B Zaugg, Yi-Hui Zhou, Joshua M Akey, Daniel Bates, Joanne Chan, Melina Claussnitzer, Kathryn Demanelis, Morgan Diegel, Jennifer A Doherty, Andrew P Feinberg, Marian S Fernando, Jessica Halow, Kasper D Hansen, Eric Haugen, Peter F Hickey, Lei Hou, Farzana Jasmine, Ruiqi Jian, Lihua Jiang, Audra Johnson, Rajinder Kaul, Manolis Kellis, Muhammad G Kibriya, Kristen Lee, Jin Billy Li, Qin Li, Jessica Lin, Shin Lin, Sandra Linder, Caroline Linke, Yaping Liu, Matthew T Maurano, Benoit Molinie, Jemma Nelson, Fidencio J Neri, Yongjin Park, Brandon L Pierce, Nicola J Rinaldi, Lindsay F Rizzardi, Richard Sandstrom, Andrew Skol, Kevin S Smith, Michael P Snyder, John Stamatoyannopoulos, Hua Tang, Li Wang, Meng Wang, Nicholas Van Wittenberghe, Fan Wu
Publication date
2017/11/1
Journal
Genome research
Volume
27
Issue
11
Pages
1843-1858
Publisher
Cold Spring Harbor Lab
Description
Gene co-expression networks capture biologically important patterns in gene expression data, enabling functional analyses of genes, discovery of biomarkers, and interpretation of genetic variants. Most network analyses to date have been limited to assessing correlation between total gene expression levels in a single tissue or small sets of tissues. Here, we built networks that additionally capture the regulation of relative isoform abundance and splicing, along with tissue-specific connections unique to each of a diverse set of tissues. We used the Genotype-Tissue Expression (GTEx) project v6 RNA sequencing data across 50 tissues and 449 individuals. First, we developed a framework called Transcriptome-Wide Networks (TWNs) for combining total expression and relative isoform levels into a single sparse network, capturing the interplay between the regulation of splicing and transcription. We built TWNs for 16 …
Scholar articles
A Saha, Y Kim, ADH Gewirtz, B Jo, C Gao, IC McDowell… - Genome research, 2017