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This article is part of the supplement: Third Annual MCBIOS Conference. Bioinformatics: A Calculated Discovery

Open Access Highly Accessed Proceedings

Beyond microarrays: Finding key transcription factors controlling signal transduction pathways

Alexdander Kel1*, Nico Voss1, Ruy Jauregui1, Olga Kel-Margoulis1 and Edgar Wingender12

Author Affiliations

1 BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany

2 Dept. Bioinformatics, UKG/Univ. Göttingen, Goldschmidtstr. 1, D-37077 Göttingen, Germany

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BMC Bioinformatics 2006, 7(Suppl 2):S13  doi:10.1186/1471-2105-7-S2-S13

Published: 26 September 2006

Abstract

Background

Massive gene expression changes in different cellular states measured by microarrays, in fact, reflect just an "echo" of real molecular processes in the cells. Transcription factors constitute a class of the regulatory molecules that typically require posttranscriptional modifications or ligand binding in order to exert their function. Therefore, such important functional changes of transcription factors are not directly visible in the microarray experiments.

Results

We developed a novel approach to find key transcription factors that may explain concerted expression changes of specific components of the signal transduction network. The approach aims at revealing evidence of positive feedback loops in the signal transduction circuits through activation of pathway-specific transcription factors. We demonstrate that promoters of genes encoding components of many known signal transduction pathways are enriched by binding sites of those transcription factors that are endpoints of the considered pathways. Application of the approach to the microarray gene expression data on TNF-alpha stimulated primary human endothelial cells helped to reveal novel key transcription factors potentially involved in the regulation of the signal transduction pathways of the cells.

Conclusion

We developed a novel computational approach for revealing key transcription factors by knowledge-based analysis of gene expression data with the help of databases on gene regulatory networks (TRANSFAC® and TRANSPATH®). The corresponding software and databases are available at http://www.gene-regulation.com webcite.