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...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Amrita Pati, Cecilia Vasquez-Robinet, Lenwood S. Heath, Ruth Grene, T. M. Murali
• Keywords: BMCBI 2006, Gene Expression, Gene Expression Data, Regulatory Motifs