Disentangling information flow in the Ras-cAMP signaling network

Genome Research
Gregory W CarterTimothy Galitski

Abstract

The perturbation of signal-transduction molecules elicits genomic-expression effects that are typically neither restricted to a small set of genes nor uniform. Instead there are broad, varied, and complex changes in expression across the genome. These observations suggest that signal transduction is not mediated by isolated pathways of information flow to distinct groups of genes in the genome. Rather, multiple entangled paths of information flow influence overlapping sets of genes. Using the Ras-cAMP pathway in Saccharomyces cerevisiae as a model system, we perturbed key pathway elements and collected genomic-expression data. Singular value decomposition was applied to separate the genome-wide transcriptional response into weighted expression components exhibited by overlapping groups of genes. Molecular interaction data were integrated to connect gene groups to perturbed signaling elements. The resulting series of linked subnetworks maps multiple putative pathways of information flow through a dense signaling network, and provides a set of testable hypotheses for complex gene-expression effects across the genome.

References

Jul 31, 1992·Science·C J Gimeno, G R Fink
Jan 7, 1998·Nature Biotechnology·L WodickaD J Lockhart
Nov 13, 1998·Proceedings of the National Academy of Sciences of the United States of America·L S Robertson, G R Fink
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Mar 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·P TamayoT R Golub
Jun 25, 1999·Pacific Symposium on Biocomputing·D C WeaverG D Stormo
Jul 13, 2000·Proceedings of the National Academy of Sciences of the United States of America·N S HolterN V Fedoroff
Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·O AlterD Botstein
May 12, 2001·FEMS Microbiology Reviews·C A D'Souza, J Heitman
Jun 8, 2001·Bioinformatics·M E WallT S Brettin
Jul 4, 2001·Nature Biotechnology·E M Marcotte
Nov 10, 2001·Annual Review of Genomics and Human Genetics·T IdekerL Hood
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·M K Stephen YeungJames J Collins
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Nov 5, 2002·BMC Bioinformatics·Martin SteffenGeorge Church
Mar 13, 2003·Proceedings of the National Academy of Sciences of the United States of America·Orly AlterDavid Botstein
Oct 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·Li LiuS Stanley Young
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young

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Citations

Aug 19, 2007·Nature Reviews. Genetics·Andreas BeyerTrey Ideker
Mar 25, 2010·PLoS Genetics·Colin A ChavelPaul J Cullen
Oct 17, 2012·PLoS Genetics·Gregory W CarterTimothy Galitski
Mar 29, 2007·Molecular Systems Biology·Gregory W CarterTimothy Galitski

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