HCVpro: Hepatitis C virus protein interaction database

Handle URI:
http://hdl.handle.net/10754/561948
Title:
HCVpro: Hepatitis C virus protein interaction database
Authors:
Kwofie, Samuel K.; Schaefer, Ulf; Sundararajan, Vijayaraghava Seshadri; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Christoffels, Alan G.
Abstract:
It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs. The use of HCVpro is free and the resource can be accessed via http://apps.sanbi.ac.za/hcvpro/ or http://cbrc.kaust.edu.sa/hcvpro/. © 2011 Elsevier B.V.
KAUST Department:
Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Applied Mathematics and Computational Science Program
Publisher:
Elsevier
Journal:
Infection, Genetics and Evolution
Issue Date:
Dec-2011
DOI:
10.1016/j.meegid.2011.09.001
PubMed ID:
21930248
Type:
Article
ISSN:
15671348
Sponsors:
This work was partly supported by grants from the National Research Foundation (South Africa), National Bioinformatics Network (to S.K.K.) and DST/NRF Research Chair (to A.C. and V.B.B.).
Appears in Collections:
Articles; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorKwofie, Samuel K.en
dc.contributor.authorSchaefer, Ulfen
dc.contributor.authorSundararajan, Vijayaraghava Seshadrien
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorChristoffels, Alan G.en
dc.date.accessioned2015-08-03T09:34:46Zen
dc.date.available2015-08-03T09:34:46Zen
dc.date.issued2011-12en
dc.identifier.issn15671348en
dc.identifier.pmid21930248en
dc.identifier.doi10.1016/j.meegid.2011.09.001en
dc.identifier.urihttp://hdl.handle.net/10754/561948en
dc.description.abstractIt is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs. The use of HCVpro is free and the resource can be accessed via http://apps.sanbi.ac.za/hcvpro/ or http://cbrc.kaust.edu.sa/hcvpro/. © 2011 Elsevier B.V.en
dc.description.sponsorshipThis work was partly supported by grants from the National Research Foundation (South Africa), National Bioinformatics Network (to S.K.K.) and DST/NRF Research Chair (to A.C. and V.B.B.).en
dc.publisherElsevieren
dc.subjectCurationen
dc.subjectDatabaseen
dc.subjectHepatitis C virusen
dc.subjectHepatocellular carcinomaen
dc.subjectNetworken
dc.subjectProtein-protein interactionen
dc.titleHCVpro: Hepatitis C virus protein interaction databaseen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentApplied Mathematics and Computational Science Programen
dc.identifier.journalInfection, Genetics and Evolutionen
dc.contributor.institutionSouth African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville 7535, Cape Town, South Africaen
kaust.authorBajic, Vladimir B.en
kaust.authorSchaefer, Ulfen

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