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The PathLinker app: Connect the dots in protein interaction networks

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dc.contributor.authorGil, Daniel P.en
dc.contributor.authorLaw, Jeffrey N.en
dc.contributor.authorMurali, T. M.en
dc.date.accessioned2020-11-03T14:26:58Zen
dc.date.available2020-11-03T14:26:58Zen
dc.date.issued2017-01-20en
dc.description.abstractPathLinker is a graph-theoretic algorithm for reconstructing the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. We originally developed PathLinker to complement manual curation of signaling pathways, which is slow and painstaking. The method can be used in general to connect any set of sources to any set of targets in an interaction network. The app presented here makes the PathLinker functionality available to Cytoscape users. We present an example where we used PathLinker to compute and analyze the network of interactions connecting proteins that are perturbed by the drug lovastatin.en
dc.description.sponsorshipThe National Institute of General Medical Sciences of the National Institutes of Health grant R01-GM095955 (TMM) and National Science Foundation (NSF) grant DBI-1062380 (TMM) supported this work.en
dc.format.extent13 pagesen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationGil DP, Law JN and Murali TM. The PathLinker app: Connect the dots in protein interaction networks [version 1; peer review: 1 approved, 2 approved with reservations] F1000Research 2017, 6:58 https://doi.org/10.12688/f1000research.9909.1en
dc.identifier.doihttps://doi.org/10.12688/f1000research.9909.1en
dc.identifier.issue58en
dc.identifier.urihttp://hdl.handle.net/10919/100778en
dc.identifier.volume6en
dc.language.isoenen
dc.publisherF1000Researchen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectsignaling pathwaysen
dc.subjectpathway reconstructionen
dc.subjectprotein interaction networksen
dc.subjectPathLinkeren
dc.subjectCytoscapeen
dc.subjectk-shortest pathsen
dc.titleThe PathLinker app: Connect the dots in protein interaction networksen
dc.title.serialF1000Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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