Identification and Confirmation of a Module of Coexpressed Genes

H. Garrett R. Thompson; Joseph W. Harris; Barbara J. Wold; Stephen R. Quake; James P. Brody

doi:10.1101/gr.418402

Identification and Confirmation of a Module of Coexpressed Genes

Departments of ¹Biology and ²Applied Physics, California Institute of Technology, Pasadena, California 91125, USA; ³Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, USA

Abstract

We synthesize a large gene expression data set using dbEST and UniGene. We use guilt-by-association (GBA) to analyze this data set and identify coexpressed genes. One module, or group of genes, was found to be coexpressed mainly in tissue extracted from breast and ovarian cancers, but also found in tissue from lung cancers, brain cancers, and bone marrow. This module contains at least six members that are believed to be involved in either transcritional regulation (PDEF, H2AFO, NUCKS) or the ubiquitin proteasome pathway (PSMD7, SQSTM1, FLJ10111). We confirm these observations of coexpression by real-time RT–PCR analysis of mRNA extracted from four model breast epithelial cell lines.