Gene interaction - An evolutionary biclustering approach

Authors:
Sushmita Mitra;Ranajit Das;Haider Banka;Subhasis Mukhopadhyay
Affiliations:
Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700 108, India;Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700 108, India;Center for Soft Computing Research, Indian Statistical Institute, Kolkata 700 108, India;Bioinformatics Center, Department of Bio-Physics, Molecular Biology and Genetics, Calcutta University, Kolkata 700 009, India
Venue:
Information Fusion
Year:
2009

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Abstract

DNA Microarray experiments form a powerful tool for studying gene expression patterns, in large scale. Sharing of the regulatory mechanism among genes, in an organism, is predominantly responsible for their co-expression. Biclustering aims at finding a subset of similarly expressed genes under a subset of experimental conditions. A small number of genes participate in a cellular process of interest. Again, a gene may be simultaneously involved in a number of cellular processes. In cellular environment, genes interact among themselves to produce enzymes, metabolites, proteins, etc. responsible for a particular function(s). In this study, a simple and novel correlation-based approach is proposed to extract gene interaction networks from biclusters in microarray data. Local search strategy is employed to add (remove) relevant (irrelevant) genes for finer tuning, in multi-objective biclustering framework. Preprocessing is done to preserve strongly correlated gene interaction pairs. Experimental results on time-series gene expression data from Yeast are biologically validated using benchmark databases and literature.