Open Access Method

Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo

Zhandong Liu12, Min Wang1, James V Alvarez1, Megan E Bonney1, Chien-chung Chen1, Celina D'Cruz1, Tien-chi Pan1, Mahlet G Tadesse3 and Lewis A Chodosh12*

Author Affiliations

1 Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, 421 Curie Blvd, BRB II/III 616, Philadelphia, PA 19104, USA

2 Genomics and Computational Biology Graduate Group, University of Pennsylvania School of Medicine, 423 Guardian Drive, Philadelphia, PA 19104, USA

3 Department of Mathematics, Georgetown University, 2115 G Street NW, Washington, DC 20057, USA

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Genome Biology 2008, 9:R180  doi:10.1186/gb-2008-9-12-r180

Published: 18 December 2008

Abstract

The ability to detect activation of signaling pathways based solely on gene expression data represents an important goal in biological research. We tested the sensitivity of singular value decomposition-based regression by focusing on functional interactions between the Ras and transforming growth factor beta signaling pathways. Our findings demonstrate that this approach is sufficiently sensitive to detect the secondary activation of endogenous signaling pathways as it occurs through crosstalk following ectopic activation of a primary pathway.