Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering.docVIP

/2002/3/11/research/0059.1 Research Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering Audrey P Gasch* and Michael B Eisen*? Addresses: *Department of Genome Science, Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. ?Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. Correspondence: Michael B Eisen. E-mail: mbeisen@ Published: 10 October 2002 Received: 1 August 2002 Revised: 6 September 2002 Accepted: 11 September 2002 GenomeBiology 2002, 3(11):research0059.1–0059.22 The electronic version of this article is the complete one and can be found online at /2002/3/11/research/0059 ? 2002 Gasch and Eisen, licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract Background: Organisms simplify the orchestration of gene expression by coregulating genes whose products function together in the cell. Many proteins serve different roles depending on the demands of the organism, and therefore the corresponding genes are often coexpressed with different groups of genes under different situations. This poses a challenge in analyzing whole- genome expression data, because many genes will be similarly expressed to multiple, distinct groups of genes. Because most commonly used analytical methods cannot appropriately represent these relationships, the connections between conditionally coregulated genes are often missed. Results: We used a heuristically modified version of fuzzy k-means clustering to identify overlapping clusters of yeast genes based on published gene-expression data following the response of yeast cells to environmental changes. We have validated the method by identifying groups of functionally related and coregulated genes, and in the process we have uncovered new correlations between yeast genes and between the experimental co