Signal transduction pathway profiling of individual tumor samples

Background: Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. Our objective is to analyze tumor gene expression data from microarrays in the context of such pathways. Results: We use pathways compiled from the TRANSPATH/TRANSFAC databases and the literature, and three publicly available cancer microarray data sets. Variation in pathway activity, across the samples, is gauged by the degree of correlation between downstream targets of a pathway. Two correlation scores are applied; one considers all pairs of downstream targets, and the other considers only pairs without common transcription factors. Several pathways are found to be differentially active in the data sets using these scores. Moreover, we devise a score for pathway activity in individual samples, based on the average expression value of the downstream targets. Statistical significance is assigned to the scores using permutation of g...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Thomas Breslin, Morten Krogh, Carsten Peterson, Carl Troein
• Keywords: BMCBI 2005, Gene Expression, Gene Expression Data, Pathway Activity