title: Gene ordering in partitive clustering using microarray expressions.
abstract: A central step in the analysis of gene expression data is the identification of groups of genes that exhibit similar expression patterns. Clustering and ordering the genes using gene expression data into homogeneous groups was shown to be useful in functional annotation, tissue classification, regulatory motif identification, and other applications. Although there is a rich literature on gene ordering in hierarchical clustering framework for gene expression analysis, there is no work addressing and evaluating the importance of gene ordering in partitive clustering framework, to the best knowledge of the authors. Outside the framework of hierarchical clustering, different gene ordering algorithms are applied on the whole data set, and the domain of partitive clustering is still unexplored with gene ordering approaches. A new hybrid method is proposed for ordering genes in each of the clusters obtained from partitive clustering solution, using microarray gene expressions.Two existing algorithms for optimally ordering cities in travelling salesman problem (TSP), namely, FRAG_GALK and Concorde, are hybridized individually with self organizing MAP to show the importance of gene ordering in partitive clustering framework. We validated our hybrid approach using yeast and fibroblast data and showed that our approach improves the result quality of partitive clustering solution, by identifying subclusters within big clusters, grouping functionally correlated genes within clusters, minimization of summation of gene expression distances, and the maximization of biological gene ordering using MIPS categorization. Moreover, the new hybrid approach, finds comparable or sometimes superior biological gene order in less computation time than those obtained by optimal leaf ordering in hierarchical clustering solution.
authors.affiliation: Center for Soft Computing Research: A National Facility, Indian Statistical Institute, Kolkata 700 108, India. shubhra_r@isical.ac.in
authors.forename: Shubhra Sankar
authors.initials: SS
authors.lastname: Ray
authors.forename: Sanghamitra
authors.initials: S
authors.lastname: Bandyopadhyay
authors.forename: Sankar K
authors.initials: SK
authors.lastname: Pal
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology*; D023061:Gene Order / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D005810:Multigene Family / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics
chemical_list: D029701:Saccharomyces cerevisiae Proteins