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dc.contributor.authorPati, Amritaen_US
dc.contributor.authorVasquez-Robinet, Ceciliaen_US
dc.contributor.authorHeath, Lenwood S.en_US
dc.contributor.authorGrene, Ruthen_US
dc.contributor.authorMurali, T. M.en_US
dc.date.accessioned2012-08-24T12:17:24Z
dc.date.available2012-08-24T12:17:24Z
dc.date.issued2006-04-21
dc.identifier.citationBMC Bioinformatics. 2006 Apr 21;7(1):218en_US
dc.identifier.urihttp://hdl.handle.net/10919/18951
dc.description.abstractBackground Modeling of cis-elements or regulatory motifs in promoter (upstream) regions of genes is a challenging computational problem. In this work, set of regulatory motifs simultaneously present in the promoters of a set of genes is modeled as a biclique in a suitably defined bipartite graph. A biologically meaningful co-occurrence of multiple cis-elements in a gene promoter is assessed by the combined analysis of genomic and gene expression data. Greater statistical significance is associated with a set of genes that shares a common set of regulatory motifs, while simultaneously exhibiting highly correlated gene expression under given experimental conditions. Methods XcisClique, the system developed in this work, is a comprehensive infrastructure that associates annotated genome and gene expression data, models known cis-elements as regular expressions, identifies maximal bicliques in a bipartite gene-motif graph; and ranks bicliques based on their computed statistical significance. Significance is a function of the probability of occurrence of those motifs in a biclique (a hypergeometric distribution), and on the new sum of absolute values statistic (SAV) that uses Spearman correlations of gene expression vectors. SAV is a statistic well-suited for this purpose as described in the discussion. Results XcisClique identifies new motif and gene combinations that might indicate as yet unidentified involvement of sets of genes in biological functions and processes. It currently supports Arabidopsis thaliana and can be adapted to other organisms, assuming the existence of annotated genomic sequences, suitable gene expression data, and identified regulatory motifs. A subset of Xcis Clique functionalities, including the motif visualization component MotifSee, source code, and supplementary material are available at https://bioinformatics.cs.vt.edu/xcisclique/.en_US
dc.format.mimetypeapplication/pdf
dc.language.isoen_US
dc.rightsCreative Commons Attribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.titleXcisClique: analysis of regulatory bicliquesen_US
dc.typeArticle - Refereed
dc.date.updated2012-08-24T12:17:24Z
dc.description.versionPeer Reviewed
dc.rights.holderAmrita Pati et al.; licensee BioMed Central Ltd.en_US
dc.contributor.departmentComputer Scienceen_US
dc.contributor.departmentSchool of Plant and Environmental Sciencesen_US
dc.title.serialBMC Bioinformatics
dc.identifier.doihttps://doi.org/10.1186/1471-2105-7-218
dc.type.dcmitypeText


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Creative Commons Attribution 4.0 International
License: Creative Commons Attribution 4.0 International