Functional association networks as priors for gene regulatory network inference

Matthew StudhamErik L L Sonnhammer


Gene regulatory network (GRN) inference reveals the influences genes have on one another in cellular regulatory systems. If the experimental data are inadequate for reliable inference of the network, informative priors have been shown to improve the accuracy of inferences. This study explores the potential of undirected, confidence-weighted networks, such as those in functional association databases, as a prior source for GRN inference. Such networks often erroneously indicate symmetric interaction between genes and may contain mostly correlation-based interaction information. Despite these drawbacks, our testing on synthetic datasets indicates that even noisy priors reflect some causal information that can improve GRN inference accuracy. Our analysis on yeast data indicates that using the functional association databases FunCoup and STRING as priors can give a small improvement in GRN inference accuracy with biological data.


Dec 26, 2001·Nucleic Acids Research·Joseph C MellorCharles DeLisi
May 7, 2004·Genome Biology·Peter M BowersDavid Eisenberg
Jul 21, 2004·Progress in Biophysics and Molecular Biology·E J CrampinP E McSharry
Nov 14, 2006·Trends in Genetics : TIG·Jesper Tegnér, Johan Björkegren
Feb 15, 2007·Molecular Systems Biology·Mukesh BansalDiego di Bernardo
Apr 6, 2007·BMC Systems Biology·Florian GeierChristian Fleck
Apr 10, 2007·Nature Genetics·Zhanzhi HuVishwanath R Iyer
Oct 11, 2007·Annals of the New York Academy of Sciences·Olivier GevaertBart De Moor
Jul 8, 2008·BMC Systems Biology·Amira Djebbari, John Quackenbush
Jan 20, 2009·Bio Systems·Michael HeckerReinhard Guthke
Apr 8, 2009·Annals of the New York Academy of Sciences·Gustavo StolovitzkyAndrea Califano
May 20, 2009·IET Systems Biology·A JuliusG J Pappas
Jun 25, 2009·EURASIP Journal on Bioinformatics & Systems Biology·Hendrik HacheRalf Herwig
Aug 28, 2009·PloS One·Scott ChristleyXiaohui Xie
Feb 27, 2010·PloS One·Robert J PrillGustavo Stolovitzky
Oct 6, 2010·BMC Systems Biology·Gökmen Altay, Frank Emmert-Streib
Nov 4, 2010·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Dec 17, 2010·Molecular BioSystems·Ritwik K LayekEdward R Dougherty
Nov 24, 2011·Nucleic Acids Research·Andrey AlexeyenkoErik L L Sonnhammer
Jun 13, 2012·Bioinformatics·Yu-Keng Shih, Srinivasan Parthasarathy
Jul 17, 2012·Nature Methods·Daniel MarbachGustavo Stolovitzky
Nov 14, 2012·Drug Discovery Today·Paola Lecca, Corrado Priami
Dec 6, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Baikang Pei, Dong-Guk Shin
Dec 12, 2012·Interface Focus·Christopher A Penfold, David L Wild
May 7, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Andreas TjärnbergErik L L Sonnhammer
Nov 5, 2013·Nucleic Acids Research·Thomas SchmittErik L L Sonnhammer
Dec 3, 2013·Systems and Synthetic Biology·Vishwesh V KulkarniMarc C Riedel


Nov 8, 2014·Molecular BioSystems·Andreas TjärnbergErik L L Sonnhammer
Oct 31, 2016·Nucleic Acids Research·Alireza F Siahpirani, Sushmita Roy
Nov 13, 2015·Science Translational Medicine·Mika GustafssonMikael Benson
Mar 16, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Doaa AltarawyLenwood S Heath
Nov 23, 2016·Statistical Applications in Genetics and Molecular Biology·Venkateshan Kannan, Jesper Tegner
Feb 15, 2018·Proceedings of the National Academy of Sciences of the United States of America·Justin D FinkleNeda Bagheri
Nov 23, 2017·Nucleic Acids Research·Christoph OgrisErik L L Sonnhammer
Dec 15, 2017·Frontiers in Immunology·Kalum ClaytonMarta E Polak
Jul 24, 2020·Journal of Bioinformatics and Computational Biology·Stephanie Kamgnia Wonkap, Gregory Butler
Dec 8, 2016·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Jul 18, 2018·Computational and Mathematical Methods in Medicine·Francisco Gómez-VelaJosé Luis Vázquez-Noguera

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