Reconstructing context-specific gene regulatory network and identifying modules and network rewiring through data integration

Methods : a Companion to Methods in Enzymology
Tianle Ma, Aidong Zhang

Abstract

Reconstructing context-specific transcriptional regulatory network is crucial for deciphering principles of regulatory mechanisms underlying various conditions. Recently studies that reconstructed transcriptional networks have focused on individual organisms or cell types and relied on data repositories of context-free regulatory relationships. Here we present a comprehensive framework to systematically derive putative regulator-target pairs in any given context by integrating context-specific transcriptional profiling and public data repositories of gene regulatory networks. Moreover, our framework can identify core regulatory modules and signature genes underlying global regulatory circuitry, and detect network rewiring and core rewired modules in different contexts by considering gene modules and edge (gene interaction) modules collaboratively. We applied our methods to analyzing Autism RNA-seq experiment data and produced biologically meaningful results. In particular, all 11 hub genes in a predicted rewired autistic regulatory subnetwork have been linked to autism based on literature review. The predicted rewired autistic regulatory network may shed some new insight into disease mechanism.

References

Apr 27, 2004·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Xiaohong GongDai Zhang
Nov 13, 2008·European Journal of Human Genetics : EJHG·Inês SousaUNKNOWN International Molecular Genetic Study of Autism Consortium (IMGSAC)
Nov 20, 2008·Bioinformatics·Xiaohui XiePierre Baldi
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Oct 24, 2009·FEBS Letters·Tobias MaierLuis Serrano
Sep 28, 2010·Brain Research·Mohammad M Ghahramani SenoStephen W Scherer
Oct 15, 2010·Nature Biotechnology·Bradley E BernsteinJames A Thomson
Dec 7, 2010·Cell·Uri David AkaviaDana Pe'er
May 27, 2011·Nature·Irina VoineaguDaniel H Geschwind
Jan 17, 2012·American Journal of Human Genetics·Viviana CaputoMarco Tartaglia
Jul 17, 2012·Nature Methods·Daniel MarbachGustavo Stolovitzky
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Mar 5, 2013·Lancet·UNKNOWN Cross-Disorder Group of the Psychiatric Genomics Consortium
Jul 25, 2013·BMC Genomics·Susan Walker, Stephen W Scherer
Jul 25, 2014·PLoS Computational Biology·Rekin's JankyStein Aerts
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Jun 13, 2015·Scientific Reports·Heonjong HanInsuk Lee
Oct 2, 2015·Database : the Journal of Biological Databases and Curation·Zhi-Ping LiuHulin Wu
Nov 26, 2015·Mental Illness·Lucia ParisiMichele Roccella
Jan 28, 2016·Molecular Biology and Evolution·Alvaro Perdomo-SabogalRobert Querfurth
Feb 3, 2016·Trends in Genetics : TIG·Jacqueline N CrawleyJanine M LaSalle
Feb 13, 2016·Scientific Reports·Nooshin OmranianZoran Nikoloski
Jul 5, 2016·Database : the Journal of Biological Databases and Curation·Andrew D RouillardAvi Ma'ayan
Sep 8, 2016·Nature·Yuta KatayamaKeiichi I Nakayama

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