Genomic analysis of regulatory network dynamics reveals large topological changes

Nature
Nicholas M LuscombeMark Gerstein

Abstract

Network analysis has been applied widely, providing a unifying language to describe disparate systems ranging from social interactions to power grids. It has recently been used in molecular biology, but so far the resulting networks have only been analysed statically. Here we present the dynamics of a biological network on a genomic scale, by integrating transcriptional regulatory information and gene-expression data for multiple conditions in Saccharomyces cerevisiae. We develop an approach for the statistical analysis of network dynamics, called SANDY, combining well-known global topological measures, local motifs and newly derived statistics. We uncover large changes in underlying network architecture that are unexpected given current viewpoints and random simulations. In response to diverse stimuli, transcription factors alter their interactions to varying degrees, thereby rewiring the network. A few transcription factors serve as permanent hubs, but most act transiently only during certain conditions. By studying sub-network structures, we show that environmental responses facilitate fast signal propagation (for example, with short regulatory cascades), whereas the cell cycle and sporulation direct temporal progression thr...Continue Reading

References

Jun 12, 1998·Nature·D J Watts, S H Strogatz
Aug 14, 1998·Molecular Cell·R J ChoR W Davis
Oct 23, 1998·Science·S ChuI Herskowitz
Oct 18, 2000·Nature·H JeongA L Barabási
Dec 5, 2000·Molecular Biology of the Cell·A P GaschP O Brown
Aug 28, 2001·Proceedings. Biological Sciences·A Wagner, D A Fell
Apr 23, 2002·Nature Genetics·Nabil GuelzimFrançois Képès
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
Oct 26, 2002·Science·Zoltán N Oltvai, Albert-László Barabási
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Dec 5, 2002·Genes & Development·Christine E HorakMichael Snyder
Feb 13, 2003·Nucleic Acids Research·M Madan Babu, Sarah A Teichmann
Mar 5, 2003·Current Opinion in Microbiology·Kenneth G Campellone, John M Leong
Jun 26, 2003·Nucleic Acids Research·M Madan Babu
Oct 24, 2003·Current Opinion in Microbiology·Agustino Martínez-Antonio, Julio Collado-Vides
Jan 22, 2004·Nature Reviews. Genetics·Albert-László Barabási, Zoltán N Oltvai
Feb 28, 2004·Science·Duncan T OdomRichard A Young
Mar 6, 2004·Science·Ron MiloUri Alon
Apr 27, 2004·Nature Genetics·Sarah A Teichmann, M Madan Babu
May 18, 2004·Trends in Genetics : TIG·Haiyuan YuMark Gerstein

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Citations

Nov 17, 2011·Journal of Molecular Medicine : Official Organ of the Gesellschaft Deutscher Naturforscher Und Ärzte·Sina A GharibDavid Gozal
Aug 2, 2007·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Tova F FullerSteve Horvath
Apr 22, 2011·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Minghui WangYuchun Pan
May 23, 2012·Bioprocess and Biosystems Engineering·Shu-Qiang Wang, Han-Xiong Li
Dec 8, 2007·Functional & Integrative Genomics·Enrico Capobianco
Oct 12, 2012·Environmental Science and Pollution Research International·Chen-Wei LiangJeng-Jong Liang
Nov 4, 2006·Bulletin of Mathematical Biology·Robert A Gatenby, B Roy Frieden
Jan 30, 2008·Cell Research·Jing-Dong Jackie Han
Aug 11, 2006·Nature Biotechnology·Yuan QiDavid K Gifford
Feb 6, 2010·Nature Protocols·Igor UlitskyRon Shamir
Apr 4, 2006·Nature Reviews. Drug Discovery·Stephen F Kingsmore
Jul 19, 2012·Nature Reviews. Genetics·Ziv Bar-JosephItamar Simon
Sep 21, 2013·Nature Reviews. Genetics·Koyel MitraTrey Ideker
Feb 24, 2006·Nature Reviews. Molecular Cell Biology·Andrew R Joyce, Bernhard Ø Palsson
Sep 22, 2005·Nature Reviews. Microbiology·Thijs J G EttemaJohn van der Oost
Mar 21, 2008·Molecular BioSystems·Christian A Grove, Albertha J M Walhout
Feb 20, 2009·Molecular BioSystems·Peddinti V GopalacharyuluMatej Oresic
Apr 28, 2009·Molecular BioSystems·Marco Cosentino LagomarsinoDaniel Remondini
Sep 19, 2009·Molecular BioSystems·Carlos Rodríguez-CasoRicard V Solé
Sep 19, 2009·Molecular BioSystems·Audrey Qiuyan Fu, Boris Adryan
Dec 22, 2009·Molecular BioSystems·Abeer FaddaKathleen Marchal
Dec 22, 2009·Molecular BioSystems·Gipsi Lima-Mendez, Jacques van Helden
Mar 20, 2010·Molecular BioSystems·Georgi MuskhelishviliMichael Berger
Mar 9, 2013·Molecular BioSystems·Sonja LehtinenVera Pancaldi
Jul 31, 2009·IET Systems Biology·M GustafssonJ Tegnér
Jun 27, 2007·IET Systems Biology·C CosentinoF Amato
Sep 22, 2006·Systems Biology·J Wildenhain, E J Crampin
Nov 27, 2008·Proceedings of the National Academy of Sciences of the United States of America·Avi Ma'ayanGustavo Stolovitzky
Jan 24, 2009·Proceedings of the National Academy of Sciences of the United States of America·Tara A GianoulisMark B Gerstein
May 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Andrew PomeranceWolfgang Losert
Jul 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Amr Ahmed, Eric P Xing
Mar 31, 2010·Proceedings of the National Academy of Sciences of the United States of America·Nitin BhardwajMark B Gerstein
May 5, 2010·Proceedings of the National Academy of Sciences of the United States of America·Koon-Kiu YanMark Gerstein
Jul 21, 2010·Proceedings of the National Academy of Sciences of the United States of America·Marina R S FortesRachel J Hawken
Oct 1, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sriram ChandrasekaranGene E Robinson

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