XcisClique: analysis of regulatory bicliques.

BMC Bioinformatics
Amrita PatiT M Murali

Abstract

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. 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-su...Continue Reading

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Citations

Jul 18, 2008·Briefings in Functional Genomics & Proteomics·Arjun Krishnan, Andy Pereira
Jul 12, 2008·PLoS Computational Biology·Loïc RoyerMichael Schroeder
Feb 23, 2010·Plant Physiology and Biochemistry : PPB·Cecilia Vásquez-RobinetRuth Grene

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Methods Mentioned

BETA
environmental stress
ChIP

Software Mentioned

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Perl
CPAN
PostgreSQL
Affymetrix MAS
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TRANSFAC

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