GEMS: A web server for biclustering analysis of expression data

Abstract

The advent of microarray technology has revolutionized the search for genes that are differentially expressed across a range of cell types or experimental conditions. Traditional clustering methods, such as hierarchical clustering, are often difficult to deploy effectively since genes rarely exhibit similar expression pattern across a wide range of conditions. Biclustering of gene expression data (also called co-clustering or two-way clustering) is a non-trivial but promising methodology for the identification of gene groups that show a coherent expression profile across a subset of conditions. Thus, biclustering is a natural methodology as a screen for genes that are functionally related, participate in the same pathways, affected by the same drug or pathological condition, or genes that form modules that are potentially co-regulated by a small group of transcription factors. We have developed a web-enabled service called GEMS (Gene Expression Mining Server) for biclustering microarray data. Users may upload expression data and specify a set of criteria. GEMS then performs bicluster mining based on a Gibbs sampling paradigm. The web server provides a flexible and an useful platform for the discovery of co-expressed and potentially co-regulated gene modules. GEMS is an open source software and is available at http://genomics10.bu.edu/terrence/gems/. © 2005 Oxford University Press.