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Article: GWASdb: A database for human genetic variants identified by genome-wide association studies

TitleGWASdb: A database for human genetic variants identified by genome-wide association studies
Authors
Issue Date2012
PublisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/
Citation
Nucleic Acids Research, 2012, v. 40 D1, p. D1047-D1054 How to Cite?
AbstractRecent advances in genome-wide association studies (GWAS) have enabled us to identify thousands of genetic variants (GVs) that are associated with human diseases. As next-generation sequencing technologies become less expensive, more GVs will be discovered in the near future. Existing databases, such as NHGRI GWAS Catalog, collect GVs with only genome-wide level significance. However, many true disease susceptibility loci have relatively moderate P values and are not included in these databases. We have developed GWASdb that contains 20 times more data than the GWAS Catalog and includes less significant GVs (P < 1.0 × 10 -3) manually curated from the literature. In addition, GWASdb provides comprehensive functional annotations for each GV, including genomic mapping information, regulatory effects (transcription factor binding sites, microRNA target sites and splicing sites), amino acid substitutions, evolution, gene expression and disease associations. Furthermore, GWASdb classifies these GVs according to diseases using Disease-Ontology Lite and Human Phenotype Ontology. It can conduct pathway enrichment and PPI network association analysis for these diseases. GWASdb provides an intuitive, multifunctional database for biologists and clinicians to explore GVs and their functional inferences. It is freely available at http://jjwanglab.org/gwasdb and will be updated frequently. © The Author(s) 2011.
Persistent Identifierhttp://hdl.handle.net/10722/148737
ISSN
2014 Impact Factor: 9.112
2014 SCImago Journal Rankings: 6.160
PubMed Central ID
ISI Accession Number ID
Funding AgencyGrant Number
University of Hong Kong201007176262
Research Grants Council of Hong Kong781511M
778609M
N_HKU752/10
Food and Health Bureau of Hong Kong10091262
National Cancer Institute (NCI), NIH, USA
Funding Information:

The Small Project Fund (201007176262) of the University of Hong Kong; Research Grants Council of Hong Kong (781511M, 778609M, N_HKU752/10); Food and Health Bureau of Hong Kong (10091262); The intramural research program of the National Cancer Institute (NCI), NIH, USA. Funding for open access charge: Research Grants Council (781511M) of Hong Kong.

References
Grants

 

DC FieldValueLanguage
dc.contributor.authorLi, MJen_HK
dc.contributor.authorWang, Pen_HK
dc.contributor.authorLiu, Xen_HK
dc.contributor.authorLim, ELen_HK
dc.contributor.authorWang, Zen_HK
dc.contributor.authorYeager, Men_HK
dc.contributor.authorWong, MPen_HK
dc.contributor.authorSham, PCen_HK
dc.contributor.authorChanock, SJen_HK
dc.contributor.authorWang, Jen_HK
dc.date.accessioned2012-05-31T07:52:33Z-
dc.date.available2012-05-31T07:52:33Z-
dc.date.issued2012en_HK
dc.identifier.citationNucleic Acids Research, 2012, v. 40 D1, p. D1047-D1054en_HK
dc.identifier.issn0305-1048en_HK
dc.identifier.urihttp://hdl.handle.net/10722/148737-
dc.description.abstractRecent advances in genome-wide association studies (GWAS) have enabled us to identify thousands of genetic variants (GVs) that are associated with human diseases. As next-generation sequencing technologies become less expensive, more GVs will be discovered in the near future. Existing databases, such as NHGRI GWAS Catalog, collect GVs with only genome-wide level significance. However, many true disease susceptibility loci have relatively moderate P values and are not included in these databases. We have developed GWASdb that contains 20 times more data than the GWAS Catalog and includes less significant GVs (P < 1.0 × 10 -3) manually curated from the literature. In addition, GWASdb provides comprehensive functional annotations for each GV, including genomic mapping information, regulatory effects (transcription factor binding sites, microRNA target sites and splicing sites), amino acid substitutions, evolution, gene expression and disease associations. Furthermore, GWASdb classifies these GVs according to diseases using Disease-Ontology Lite and Human Phenotype Ontology. It can conduct pathway enrichment and PPI network association analysis for these diseases. GWASdb provides an intuitive, multifunctional database for biologists and clinicians to explore GVs and their functional inferences. It is freely available at http://jjwanglab.org/gwasdb and will be updated frequently. © The Author(s) 2011.en_HK
dc.languageeng-
dc.publisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/en_HK
dc.relation.ispartofNucleic Acids Researchen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleGWASdb: A database for human genetic variants identified by genome-wide association studiesen_HK
dc.typeArticleen_HK
dc.identifier.emailSham, PC: pcsham@hku.hken_HK
dc.identifier.emailWang, J: junwen@hku.hken_HK
dc.identifier.authoritySham, PC=rp00459en_HK
dc.identifier.authorityWang, J=rp00280en_HK
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1093/nar/gkr1182en_HK
dc.identifier.pmid22139925en_HK
dc.identifier.pmcidPMC3245026-
dc.identifier.scopuseid_2-s2.0-84861023442en_HK
dc.identifier.hkuros208295-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-84861023442&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume40en_HK
dc.identifier.issueD1en_HK
dc.identifier.spageD1047en_HK
dc.identifier.epageD1054en_HK
dc.identifier.eissn1362-4962-
dc.identifier.isiWOS:000298601300157-
dc.publisher.placeUnited Kingdomen_HK
dc.relation.projectA Novel Hidden Markov Model to Predict microRNAs and their Targets Simultaneously and its Application to the Epstein-Barr virus-
dc.identifier.scopusauthoridLi, MJ=37008547900en_HK
dc.identifier.scopusauthoridWang, P=54397871300en_HK
dc.identifier.scopusauthoridLiu, X=55249909900en_HK
dc.identifier.scopusauthoridLim, EL=55249666000en_HK
dc.identifier.scopusauthoridWang, Z=55250397100en_HK
dc.identifier.scopusauthoridYeager, M=55162828300en_HK
dc.identifier.scopusauthoridWong, MP=55250969600en_HK
dc.identifier.scopusauthoridSham, PC=34573429300en_HK
dc.identifier.scopusauthoridChanock, SJ=55163287400en_HK
dc.identifier.scopusauthoridWang, J=8950599500en_HK
dc.identifier.citeulike10142837-

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