title: TCLUST: a fast method for clustering genome-scale expression data.
abstract: Genes with a common function are often hypothesized to have correlated expression levels in mRNA expression data, motivating the development of clustering algorithms for gene expression data sets. We observe that existing approaches do not scale well for large data sets, and indeed did not converge for the data set considered here. We present a novel clustering method TCLUST that exploits coconnectedness to efficiently cluster large, sparse expression data. We compare our approach with two existing clustering methods CAST and K-means which have been previously applied to clustering of gene-expression data with good performance results. Using a number of metrics, TCLUST is shown to be superior to or at least competitive with the other methods, while being much faster. We have applied this clustering algorithm to a genome-scale gene-expression data set and used gene set enrichment analysis to discover highly significant biological clusters. (Source code for TCLUST is downloadable at http://www.cse.ucsd.edu/~bdost/tclust.)
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego, CA 92093, USA. bdost@cs.ucsd.edu
authors.forename: Banu
authors.initials: B
authors.lastname: Dost
authors.forename: Chunlei
authors.initials: C
authors.lastname: Wu
authors.forename: Andrew
authors.initials: A
authors.lastname: Su
authors.forename: Vineet
authors.initials: V
authors.lastname: Bafna
mesh_terms: D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D003198:Computer Simulation; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods*; D051379:Mice; D008815:Mice, Inbred Strains; D008958:Models, Molecular; D020411:Oligonucleotide Array Sequence Analysis