dc.contributor.author | Parikh, Jignesh R. | |
dc.contributor.author | Xia, Yu | |
dc.contributor.author | Marto, Jarrod | |
dc.date.accessioned | 2013-04-05T14:44:18Z | |
dc.date.issued | 2012 | |
dc.identifier.citation | Parikh, 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.issn | 1932-6203 | en_US |
dc.identifier.uri | http://nrs.harvard.edu/urn-3:HUL.InstRepos:10498783 | |
dc.description.abstract | Curated 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.iso | en_US | en_US |
dc.publisher | Public Library of Science | en_US |
dc.relation.isversionof | doi:10.1371/journal.pone.0045211 | en_US |
dc.relation.hasversion | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3441533/pdf/ | en_US |
dash.license | LAA | |
dc.subject | Biology | en_US |
dc.subject | Computational Biology | en_US |
dc.subject | Genomics | en_US |
dc.subject | Genome Analysis Tools | en_US |
dc.subject | Genetic Networks | en_US |
dc.subject | Biological Data Management | en_US |
dc.subject | Microarrays | en_US |
dc.subject | Regulatory Networks | en_US |
dc.subject | Signaling Networks | en_US |
dc.subject | Molecular Cell Biology | en_US |
dc.subject | Signal Transduction | en_US |
dc.subject | Signaling Pathways | en_US |
dc.subject | Gene Expression | en_US |
dc.subject | Computer Science | en_US |
dc.subject | Algorithms | en_US |
dc.subject | Computer Applications | en_US |
dc.subject | Web-Based Applications | en_US |
dc.title | Multi-Edge Gene Set Networks Reveal Novel Insights into Global Relationships between Biological Themes | en_US |
dc.type | Journal Article | en_US |
dc.description.version | Version of Record | en_US |
dc.relation.journal | PLoS ONE | en_US |
dash.depositing.author | Marto, Jarrod | |
dc.date.available | 2013-04-05T14:44:18Z | |
dc.identifier.doi | 10.1371/journal.pone.0045211 | * |
dash.contributor.affiliated | Marto, Jarrod | |