XcisClique: analysis of regulatory bicliques

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XcisClique: analysis of regulatory bicliques
Background: 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 signific...
Amrita Pati, Cecilia Vasquez-Robinet, Lenwood S. H
Added 10 Dec 2010
Updated 10 Dec 2010
Type Journal
Year 2006
Authors Amrita Pati, Cecilia Vasquez-Robinet, Lenwood S. Heath, Ruth Grene, T. M. Murali
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