Using Bayesian networks to analyze expression data

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Nir FriedmanDana Pe'er

Abstract

DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a "snapshot" of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biological features of cellular systems. In this paper, we propose a new framework for discovering interactions between genes based on multiple expression measurements. This framework builds on the use of Bayesian networks for representing statistical dependencies. A Bayesian network is a graph-based model of joint multivariate probability distributions that captures properties of conditional independence between variables. Such models are attractive for their ability to describe complex stochastic processes and because they provide a clear methodology for learning from (noisy) observations. We start by showing how Bayesian networks can describe interactions between genes. We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cell-cycle measurements of Spellman et al. (1998).

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Oct 10, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·J KimKwang-Hyun Cho
Oct 5, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Li-Zhi LiuW J Zhang
Dec 7, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Haseong Kim, Erol Gelenbe
Feb 22, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Amina NoorHazem N Nounou
May 2, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiuwei Zhang, Bernard M E Moret
Jun 8, 2013·IEEE Transactions on Bio-medical Engineering·Fang-Han HsuErchin Serpedin
Mar 13, 2014·IEEE Journal of Biomedical and Health Informatics·K KalantzakiD I Fotiadis
Apr 1, 2014·IEEE Transactions on Biomedical Circuits and Systems·Maryam Masnadi-ShiraziShankar Subramaniam
Jun 6, 2012·IEEE Transactions on Pattern Analysis and Machine Intelligence·Shuai HuangAlzheimer’s Disease Neuroimaging Initiative
May 25, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Carlos H A HigaRonaldo F Hashimoto
Feb 22, 2014·IEEE Transactions on Bio-medical Engineering·Anwoy MohantyVijayanagaram Venkatraj
Mar 1, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Kristopher L PattonGloria K Muday
May 9, 2014·IEEE Journal of Biomedical and Health Informatics·G SkretiM Zervakis
Oct 15, 2014·IEEE Transactions on Nanobioscience·Aniruddha MaitiAnirban Mukherjee
Aug 1, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ngoc Tu LeBich Hai Ho
Aug 18, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yoshinori TamadaS Miyano
Oct 19, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Samuel KaskiChristophe Roos
May 3, 2008·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Wentao ZhaoEdward R Dougherty
Dec 12, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Hazem N NounouEdward R Dougherty
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May 2, 2009·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yongjin ParkRussell Schwartz
Apr 6, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Martin HopfensitzHans A Kestler
Nov 3, 2007·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Rui XuRonald Frank
Nov 3, 2007·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Shinn-Ying HoHui-Ling Huang
Nov 3, 2007·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ignacio PonzoniDavid Glass
May 13, 2005·Bio Systems·Kwang-Hyun ChoOlaf Wolkenhauer
Jan 15, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ramesh Ram, Madhu Chetty
Oct 21, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jieping YeRavi Janardan
Nov 13, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Mehmet TanFaruk Polat
Nov 13, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Sushmita MitraYoichi Hayashi
May 18, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Kyriakos Kentzoglanakis, Matthew Poole
Nov 13, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Nathan A BarkerHiroyuki Kuwahara
May 19, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·André FujitaS Miyano
Feb 2, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Rui ChangWei Wang
Sep 22, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·David J JohnJames L Norris
Sep 22, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Erdem YörükLaurent Younes
Oct 1, 2009·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Liping JingYing Liu
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Apr 20, 2007·IEEE Engineering in Medicine and Biology Magazine : the Quarterly Magazine of the Engineering in Medicine & Biology Society·Alireza Tamaddoni-NezhadStephen Muggleton
May 9, 2009·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Rubén ArmañanzasAna M Zubiaga
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Sep 8, 2004·Bio Systems·R Eriksson, B Olsson
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Jan 5, 2010·IEEE Signal Processing Magazine·Yufei HuangYufeng Wang
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Nov 16, 2011·IEEE Transactions on Neural Systems and Rehabilitation Engineering : a Publication of the IEEE Engineering in Medicine and Biology Society·Heather L BenzNitish V Thakor
Jun 29, 2004·Artificial Intelligence in Medicine·Changwon Yoo, Gregory F Cooper
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Jun 29, 2004·Artificial Intelligence in Medicine·Iñaki InzaAntonio J Cerrolaza
Mar 15, 2015·IEEE Journal of Biomedical and Health Informatics·Anwoy MohantyJijayanagaram Venkatraj
Oct 10, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Sanchit MisraSrinivas Aluru
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Nov 22, 2015·BMC Systems Biology·Mahsa GhanbariMartin Vingron
Aug 13, 2005·Journal of Theoretical Biology·A P Quayle, S Bullock
Jun 28, 2005·Computers in Biology and Medicine·Yonghong Peng
Jul 16, 2013·IET Systems Biology·Manoj KandpalLakshminarayanan Samavedham
Jan 24, 2006·Accident; Analysis and Prevention·Kaan Ozbay, Nebahat Noyan
Apr 6, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Nitin Singh, Mathukumalli Vidyasagar
Apr 22, 2015·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Rui-Sheng WangJoseph Loscalzo
Apr 3, 2014·Evidence-based Complementary and Alternative Medicine : ECAM·Hsin-Chieh Tang, Calvin Yu-Chian Chen
Mar 19, 2013·Bio Systems·Luis A FuenteAndy M Tyrrell
Apr 9, 2013·Artificial Intelligence in Medicine·Pablo Hernandez-LealL Enrique Sucar
Aug 20, 2014·Evidence-based Complementary and Alternative Medicine : ECAM·Ya-Li HsiaoCalvin Yu-Chian Chen
Jan 3, 2014·Artificial Intelligence in Medicine·Lucia SacchiStephen Swift
Jun 5, 2015·BMC Systems Biology·Jakob WieczorekKatja Ickstadt
Apr 29, 2015·BMC Bioinformatics·Ernst C Wit, Antonino Abbruzzo
Oct 23, 2004·Journal of Theoretical Biology·Madhukar S DasikaCostas D Maranas
Oct 20, 2004·Metabolic Engineering·Sarika MehraGeorge Karypis
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Dec 21, 2010·Bio Systems·Zaher DawyHady Ali Zeineddine
Jun 29, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Jennifer ClarkeNagi G Ayad
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Dec 20, 2011·Journal of Biomedical Informatics·F K AhmadN H Othman
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Jan 24, 2009·Journal of Biomedical Informatics·Hong-Qiang WangTimothy T C Yip
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Mar 19, 2014·Journal of Theoretical Biology·Yunjun ZhangZhi Geng
Mar 25, 2014·Seminars in Cancer Biology·Ali Masoudi-NejadEdwin Wang
Jul 12, 2011·Computers in Biology and Medicine·Qing ZhangDianjing Guo
Nov 30, 2014·Progress in Biophysics and Molecular Biology·James ParkRajanikanth Vadigepalli
Dec 4, 2014·Pathophysiology : the Official Journal of the International Society for Pathophysiology·Li M Fu, Katherine A Fu
Oct 9, 2014·Annual Review of Pharmacology and Toxicology·Heung-Woo ParkScott T Weiss
Jul 26, 2014·Journal of the American Statistical Association·Hulin WuHua Liang
May 6, 2016·Scientific Reports·Harold BaeP Sebastiani
Jan 23, 2015·PLoS Computational Biology·Daeyong Jin, Hyunju Lee
May 22, 2016·Nucleic Acids Research·Junko YamaneWataru Fujibuchi
May 15, 2016·Bio Systems·Yoli ShavitHillel Kugler
May 26, 2016·Gene·Prantik Chatterjee, Nikhil Ranjan Pal
Sep 14, 2016·Iranian Red Crescent Medical Journal·Hamid Alavi MajdNasibeh Khayyer
Nov 5, 2014·PloS One·Djordje DjordjevicJoshua W K Ho
Sep 29, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Rami Al-DalkyMurad Qasaimeh
Jun 17, 2016·Bioinformatics·Yue DengLani F Wu