Discovering phenotype specific gene module using a novel biclustering algorithm in colorectal cancer

Abstract

Gene clustering is a method for finding gene sets which are related to the same biological processes or molecular function. In order to find these gene sets, previous studies have clustered genes which showed similar mRNA expression or a specific expression pattern in a (sub) sample set. However, for two contrasting groups of samples, it is not easy to identify gene sets which show significant expression pattern in only one group using current gene clustering methods. Existing biclustering methods use only one group (disease) of samples. It is hard to identify disease specific biclusters which are differentially expressed in the disease although those methods can find biclusters which have specific expression pattern. Here, we proposed a novel method using a genetic algorithm in gene expression data, in order to find gene sets which can represent specific subtype of cancer. Proposed method finds gene sets which have statistically differential mRNA expression on two contrasting samples and fraction of cancer samples. The resulting gene modules share higher number of GO (Gene Ontology) terms related to a specific disease than gene modules identified by current algorithms. We also identify that when we integrate protein-protein interaction data with gene expression data of colorectal cancer samples, proposed method can find more functionally related gene sets. © 2014 IEEE.