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dc.contributor.authorParikh, Jignesh R.
dc.contributor.authorXia, Yu
dc.contributor.authorMarto, Jarrod
dc.date.accessioned2013-04-05T14:44:18Z
dc.date.issued2012
dc.identifier.citationParikh, Jignesh R., Yu Xia, and Jarrod A. Marto. 2012. Multi-edge gene set networks reveal novel insights into global relationships between biological themes. PLoS ONE 7(9): e45211.en_US
dc.identifier.issn1932-6203en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:10498783
dc.description.abstractCurated gene sets from databases such as KEGG Pathway and Gene Ontology are often used to systematically organize lists of genes or proteins derived from high-throughput data. However, the information content inherent to some relationships between the interrogated gene sets, such as pathway crosstalk, is often underutilized. A gene set network, where nodes representing individual gene sets such as KEGG pathways are connected to indicate a functional dependency, is well suited to visualize and analyze global gene set relationships. Here we introduce a novel gene set network construction algorithm that integrates gene lists derived from high-throughput experiments with curated gene sets to construct co-enrichment gene set networks. Along with previously described co-membership and linkage algorithms, we apply the co-enrichment algorithm to eight gene set collections to construct integrated multi-evidence gene set networks with multiple edge types connecting gene sets. We demonstrate the utility of approach through examples of novel gene set networks such as the chromosome map co-differential expression gene set network. A total of twenty-four gene set networks are exposed via a web tool called MetaNet, where context-specific multi-edge gene set networks are constructed from enriched gene sets within user-defined gene lists. MetaNet is freely available at http://blaispathways.dfci.harvard.edu/metanet/.en_US
dc.language.isoen_USen_US
dc.publisherPublic Library of Scienceen_US
dc.relation.isversionofdoi:10.1371/journal.pone.0045211en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3441533/pdf/en_US
dash.licenseLAA
dc.subjectBiologyen_US
dc.subjectComputational Biologyen_US
dc.subjectGenomicsen_US
dc.subjectGenome Analysis Toolsen_US
dc.subjectGenetic Networksen_US
dc.subjectBiological Data Managementen_US
dc.subjectMicroarraysen_US
dc.subjectRegulatory Networksen_US
dc.subjectSignaling Networksen_US
dc.subjectMolecular Cell Biologyen_US
dc.subjectSignal Transductionen_US
dc.subjectSignaling Pathwaysen_US
dc.subjectGene Expressionen_US
dc.subjectComputer Scienceen_US
dc.subjectAlgorithmsen_US
dc.subjectComputer Applicationsen_US
dc.subjectWeb-Based Applicationsen_US
dc.titleMulti-Edge Gene Set Networks Reveal Novel Insights into Global Relationships between Biological Themesen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalPLoS ONEen_US
dash.depositing.authorMarto, Jarrod
dc.date.available2013-04-05T14:44:18Z
dc.identifier.doi10.1371/journal.pone.0045211*
dash.contributor.affiliatedMarto, Jarrod


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