Analysis of promoter regions of co-expressed genes identified by microarray analysis

Background: The use of global gene expression profiling to identify sets of genes with similar expression patterns is rapidly becoming a widespread approach for understanding biological processes. A logical and systematic approach to study co-expressed genes is to analyze their promoter sequences to identify transcription factors that may be involved in establishing specific profiles and that may be experimentally investigated. Results: We introduce promoter clustering i.e. grouping of promoters with respect to their high scoring motif content, and show that this approach greatly enhances the identification of common and significant transcription factor binding sites (TFBS) in co-expressed genes. We apply this method to two different dataset, one consisting of micro array data from 108 leukemias (AMLs) and a second from a time series experiment, and show that biologically relevant promoter patterns may be obtained using phylogenetic foot-printing methodology. In addition, we also foun...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Srinivas Veerla, Mattias Höglund
• Keywords: BMCBI 2006, Gene Expression, Promoter, Transcription Factors