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CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining

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dc.contributor.authorPati, Amritaen
dc.contributor.authorJin, Yingen
dc.contributor.authorKlage, Karstenen
dc.contributor.authorHelm, Richard F.en
dc.contributor.authorHeath, Lenwood S.en
dc.contributor.authorRamakrishnan, Narenen
dc.contributor.departmentBiochemistryen
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2017-01-04T15:17:17Zen
dc.date.available2017-01-04T15:17:17Zen
dc.date.issued2008-01-01en
dc.description.abstractCMGSDB (Database for Computational Modeling of Gene Silencing) is an integration of heterogeneous data sources about Caenorhabditis elegans with capabilities for compositional data mining (CDM) across diverse domains. Besides gene, protein and functional annotations, CMGSDB currently unifies information about 531 RNAi phenotypes obtained from heterogeneous databases using a hierarchical scheme. A phenotype browser at the CMGSDB website serves this hierarchy and relates phenotypes to other biological entities. The application of CDM to CMGSDB produces ‘chains’ of relationships in the data by finding two-way connections between sets of biological entities. Chains can, for example, relate the knock down of a set of genes during an RNAi experiment to the disruption of a pathway or specific gene expression through another set of genes not directly related to the former set. The web interface for CMGSDB is available at https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/, and serves individual biological entity information as well as details of all chains computed by CDM.en
dc.description.versionPublished versionen
dc.format.extentD69 - D76 (8) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gkm804en
dc.identifier.issn0305-1048en
dc.identifier.urihttp://hdl.handle.net/10919/73934en
dc.identifier.volume36en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000252545400013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution-NonCommercial 2.0 UK: England & Walesen
dc.rights.holderThe Author(s)en
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.0/uk/en
dc.subjectBiochemistry & Molecular Biologyen
dc.subjectGENOME-WIDE RNAIen
dc.subjectC-ELEGANSen
dc.subjectGENESen
dc.subjectSCREENen
dc.subjectINTERFERENCEen
dc.subjectLOCALIZATIONen
dc.subjectEMBRYOSen
dc.subjectRECEPTORen
dc.subjectEMBRYOGENESISen
dc.subjectESTABLISHMENTen
dc.titleCMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data miningen
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Biochemistryen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineeringen
pubs.organisational-group/Virginia Tech/Engineering/COE T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineering/Computer Scienceen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen

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