Biclustering in gene expression data by tendency

Abstract

The advent of DNA microarray technologies has revolutionized the experimental study of gene expression. Clustering is the most popular approach of analyzing gene expression data and has indeed proven to be successful in many applications. Our work focuses on discovering a subset of genes which exhibit similar expression patterns along a subset of conditions in the gene expression matrix. Specifically, we are looking for the Order Preserving clusters (OPCluster), in each of which a subset of genes induce a similar linear ordering along a subset of conditions. The pioneering work of the OPSM model[3], which enforces the strict order shared by the genes in a cluster, is included in our model as a special case. Our model is more robust than OPSM because similarly expressed conditions are allowed to form order equivalent groups and no restriction is placed on the order within a group. Guided by our model, we design and implement a deterministic algorithm, namely OPCTree, to discover OP-Clusters. Experimental study on two real datasets demonstrates the effectiveness of the algorithm in the application of tissue classification and cell cycle identification. In addition, a large percentage of OP-Clusters exhibit significant enrichment of one or more function categories, which implies that OP-Clusters indeed carry significant biological relevance.