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dc.contributor.authorParikh, Jignesh R.en_US
dc.contributor.authorKlinger, Bertramen_US
dc.contributor.authorXia, Yuen_US
dc.contributor.authorMarto, Jarrod A.en_US
dc.contributor.authorBlüthgen, Nilsen_US
dc.date.accessioned2012-01-11T00:40:40Z
dc.date.available2012-01-11T00:40:40Z
dc.date.copyright2010en_US
dc.date.issued2010-5-21en_US
dc.identifier.citationParikh, 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.issn1362-4962en_US
dc.identifier.urihttp://hdl.handle.net/2144/3035
dc.description.abstractHigh-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.sponsorshipGermany'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.isoenen_US
dc.publisherOxford University Pressen_US
dc.rightsCopyright Parikh, Jignesh R., Bertram Klinger, Yu Xia, Jarrod A. Marto, Nils Blüthgen 2010. Published by Oxford University Press.en_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.5en_US
dc.titleDiscovering Causal Signaling Pathways through Gene-Expression Patternsen_US
dc.typearticleen_US
dc.identifier.doi10.1093/nar/gkq424en_US
dc.identifier.pubmedid20494976en_US
dc.identifier.pmcid2896193en_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.