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Discovering Causal Signaling Pathways through Gene-Expression Patterns

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dc.contributor.author Parikh, Jignesh R. en_US
dc.contributor.author Klinger, Bertram en_US
dc.contributor.author Xia, Yu en_US
dc.contributor.author Marto, Jarrod A. en_US
dc.contributor.author Blüthgen, Nils en_US
dc.date.accessioned 2012-01-11T00:40:40Z
dc.date.available 2012-01-11T00:40:40Z
dc.date.copyright 2010 en_US
dc.date.issued 2010-5-21 en_US
dc.identifier.citation Parikh, Jignesh R., Bertram Klinger, Yu Xia, Jarrod A. Marto, Nils Blüthgen. "Discovering causal signaling pathways through gene-expression patterns" Nucleic Acids Research 38(Web Server issue): W109-W117. (2010) en_US
dc.identifier.issn 1362-4962 en_US
dc.identifier.uri http://hdl.handle.net/2144/3035
dc.description.abstract High-throughput gene-expression studies result in lists of differentially expressed genes. Most current meta-analyses of these gene lists include searching for significant membership of the translated proteins in various signaling pathways. However, such membership enrichment algorithms do not provide insight into which pathways caused the genes to be differentially expressed in the first place. Here, we present an intuitive approach for discovering upstream signaling pathways responsible for regulating these differentially expressed genes. We identify consistently regulated signature genes specific for signal transduction pathways from a panel of single-pathway perturbation experiments. An algorithm that detects overrepresentation of these signature genes in a gene group of interest is used to infer the signaling pathway responsible for regulation. We expose our novel resource and algorithm through a web server called SPEED: Signaling Pathway Enrichment using Experimental Data sets. SPEED can be freely accessed at http://speed.sys-bio.net/. en_US
dc.description.sponsorship Germany's Federal Ministry for Education and Research; the European Commission (CancerSys HEALTHF4-2008-223188); National Science Foundation Integrative Graduate Education and Research Traineeship (DGE-0654108) en_US
dc.language.iso en en_US
dc.publisher Oxford University Press en_US
dc.rights Copyright Parikh, Jignesh R., Bertram Klinger, Yu Xia, Jarrod A. Marto, Nils Blüthgen 2010. Published by Oxford University Press. en_US
dc.rights.uri http://creativecommons.org/licenses/by-nc/2.5 en_US
dc.title Discovering Causal Signaling Pathways through Gene-Expression Patterns en_US
dc.type article en_US
dc.identifier.doi 10.1093/nar/gkq424 en_US
dc.identifier.pubmedid 20494976 en_US
dc.identifier.pmcid 2896193 en_US


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Copyright Parikh, Jignesh R., Bertram Klinger, Yu Xia, Jarrod A. Marto, Nils Blüthgen 2010. Published by Oxford University Press. Except where otherwise noted, this item's license is described as Copyright Parikh, Jignesh R., Bertram Klinger, Yu Xia, Jarrod A. Marto, Nils Blüthgen 2010. Published by Oxford University Press.

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