MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences

Bioinformatics
Phil ArnoldErik van Nimwegen

Abstract

Probabilistic approaches for inferring transcription factor binding sites (TFBSs) and regulatory motifs from DNA sequences have been developed for over two decades. Previous work has shown that prediction accuracy can be significantly improved by incorporating features such as the competition of multiple transcription factors (TFs) for binding to nearby sites, the tendency of TFBSs for co-regulated TFs to cluster and form cis-regulatory modules and explicit evolutionary modeling of conservation of TFBSs across orthologous sequences. However, currently available tools only incorporate some of these features, and significant methodological hurdles hampered their synthesis into a single consistent probabilistic framework. We present MotEvo, a integrated suite of Bayesian probabilistic methods for the prediction of TFBSs and inference of regulatory motifs from multiple alignments of phylogenetically related DNA sequences, which incorporates all features just mentioned. In addition, MotEvo incorporates a novel model for detecting unknown functional elements that are under evolutionary constraint, and a new robust model for treating gain and loss of TFBSs along a phylogeny. Rigorous benchmarking tests on ChIP-seq datasets show that M...Continue Reading

References

Oct 25, 1990·Nucleic Acids Research·T D Schneider, R M Stephens
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Jul 10, 1998·Molecular Biology and Evolution·A L Halpern, W J Bruno
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Oct 24, 2001·Bioinformatics·M C FrithZ Weng
Jul 12, 2003·Bioinformatics·Saurabh SinhaEric D Siggia
Aug 14, 2003·Science's STKE : Signal Transduction Knowledge Environment·Kevin M McBride, Nancy C Reich
Aug 14, 2003·The Journal of Pediatrics·Richard A Polin
Oct 30, 2004·BMC Bioinformatics·Saurabh SinhaMartin Tompa
Feb 8, 2005·Journal of Cellular Biochemistry·David N Arnosti, Meghana M Kulkarni
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Dec 31, 2005·Nucleic Acids Research·Dominique VliegheBoris Lenhard
Feb 16, 2006·PLoS Computational Biology·Rahul SiddharthanErik van Nimwegen
Nov 14, 2006·Bioinformatics·Helge G RoiderMartin Vingron
Jan 25, 2007·Algorithms for Molecular Biology : AMB·C Steven CarmackCharles E Lawrence
Jun 30, 2007·BMC Bioinformatics·Marc A Marti-RenomAndrej Sali
Jul 13, 2007·BMC Bioinformatics·Adriana Climescu-Haulica, Michelle D Quirk
Jul 10, 2007·PLoS Genetics·Eimear E HolohanRobert White
Nov 23, 2007·Genome Research·Nacho Molina, Erik van Nimwegen
Dec 19, 2007·Nucleic Acids Research·D KarolchikW J Kent
Aug 8, 2008·Nucleic Acids Research·Raja JothiKeji Zhao
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Apr 21, 2009·Nature Genetics·UNKNOWN FANTOM ConsortiumYoshihide Hayashizaki
May 30, 2009·Bioinformatics·John HawkinsTimothy L Bailey
Sep 2, 2009·Genome Research·Todd Wasson, Alexander J Hartemink
Jun 24, 2010·Molecular Systems Biology·Bartek Wilczyński, Eileen E M Furlong
Jul 31, 2010·Quality & Safety in Health Care·N L WilczynskiUNKNOWN QI Hedges Team
Sep 11, 2010·Genome Biology and Evolution·Kevin ChenMark L Siegal

❮ Previous
Next ❯

Citations

Nov 28, 2012·Nucleic Acids Research·Mikhail PachkovErik van Nimwegen
Feb 12, 2014·Genome Research·Piotr J BalwierzErik van Nimwegen
Nov 29, 2015·Nucleic Acids Research·UNKNOWN SIB Swiss Institute of Bioinformatics Members
Aug 9, 2015·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Michiel de HoonPiero Carninci
Jul 15, 2015·Methods : a Companion to Methods in Enzymology·Peter J Pemberton-RossErik van Nimwegen
Dec 30, 2014·BMC Genomics·Morana VitezicAlka Saxena
Apr 8, 2014·Molecular Genetics and Metabolism·Margaret R DavisUNKNOWN FANTOM Consortium
Jun 3, 2016·Frontiers in Physiology·Sergio A Alcalá-CoronaEnrique Hernández-Lemus
Mar 24, 2017·Molecular Genetics and Genomics : MGG·Juan M Calvo-MartínCarmen Segarra
Aug 13, 2015·Nutrients·Johannes OldenburgCarville G Bevans
Nov 22, 2014·Nature Communications·Andreas R GruberMihaela Zavolan
Jan 17, 2017·Scientific Reports·Regula FurrerChristoph Handschin
May 18, 2016·Molecular Endocrinology·Silvia SalatinoChristoph Handschin
Aug 23, 2017·Nature Biotechnology·Derek de RieMichiel J L de Hoon
May 30, 2019·Genome Research·Severin BergerErik van Nimwegen
Sep 14, 2012·G3 : Genes - Genomes - Genetics·Andrew T KwonWyeth W Wasserman
Feb 7, 2016·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Kristoffer SvenssonChristoph Handschin
Jul 29, 2020·Genome Research·Tanvir AlamMichiel J L de Hoon
Oct 12, 2013·Bioinformatics·Matthew Levinson, Qing Zhou
May 13, 2017·BioMed Research International·Haitao Guo, Hongwei Huo
Oct 5, 2021·PLoS Computational Biology·Sergio SarnataroNacho Molina
Nov 1, 2021·Human Molecular Genetics·Matthew R J MasonJoost Verhaagen

❮ Previous
Next ❯

Related Concepts

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.