{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:40:24Z","timestamp":1675291224090},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":357,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,15]]},"abstract":"Abstract<\/jats:title>\n Summary: As the volume of patient-specific genome sequences increases the focus of biomedical research is switching from the detection of disease-mutations to their interpretation. To this end a number of techniques have been developed that use mutation data collected within a population to predict whether individual genes are likely to be disease-causing or not. As both sequence data and associated analysis tools proliferate, it becomes increasingly difficult for the community to make sense of these data and their implications. Moreover, no single analysis tool is likely to capture all relevant genomic features that contribute to the gene\u2019s pathogenicity. Here, we introduce Web-based Gene Pathogenicity Analysis (WGPA), a web-based tool to analyze genes impacted by mutations and rank them through the integration of existing prioritization tools, which assess different aspects of gene pathogenicity using population-level sequence data. Additionally, to explore the polygenic contribution of mutations to disease, WGPA implements gene set enrichment analysis to prioritize disease-causing genes and gene interaction networks, therefore providing a comprehensive annotation of personal genomes data in disease.<\/jats:p>\n Availability and implementation: wgpa.systems-genetics.net<\/jats:p>\n Contact: \u00a0enrico.petretto@duke-nus.edu.sg<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv598","type":"journal-article","created":{"date-parts":[[2015,10,22]],"date-time":"2015-10-22T01:39:39Z","timestamp":1445477979000},"page":"635-637","source":"Crossref","is-referenced-by-count":1,"title":["Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data"],"prefix":"10.1093","volume":"32","author":[{"given":"Juan J.","family":"Diaz-Montana","sequence":"first","affiliation":[{"name":"1 School of Engineering, Pablo de Olavide University, Seville, 41013 Spain and"}]},{"given":"Owen J.L.","family":"Rackham","sequence":"additional","affiliation":[{"name":"2 Duke-NUS Graduate Medical School Singapore, Singapore, 169857 Singapore"}]},{"given":"Norberto","family":"Diaz-Diaz","sequence":"additional","affiliation":[{"name":"1 School of Engineering, Pablo de Olavide University, Seville, 41013 Spain and"}]},{"given":"Enrico","family":"Petretto","sequence":"additional","affiliation":[{"name":"2 Duke-NUS Graduate Medical School Singapore, Singapore, 169857 Singapore"}]}],"member":"286","published-online":{"date-parts":[[2015,10,21]]},"reference":[{"key":"2023020110351996300_btv598-B1","doi-asserted-by":"crossref","DOI":"10.1002\/0471142905.hg0720s76","volume-title":"Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2.","author":"Adzhubei","year":"2013"},{"key":"2023020110351996300_btv598-B2","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/nature12439","article-title":"De\u00a0novo mutations in epileptic encephalopathies","volume":"501","author":"Allen","year":"2013","journal-title":"Nature"},{"key":"2023020110351996300_btv598-B3","first-page":"751","article-title":"Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway","volume":"16","author":"Enns","year":"2014","journal-title":"Genet. Med. Off. J. Am. Coll. Med. Genet."},{"key":"2023020110351996300_btv598-B4","doi-asserted-by":"crossref","first-page":"e1003709","DOI":"10.1371\/journal.pgen.1003709","article-title":"Genic intolerance to functional variation and the interpretation of personal genomes","volume":"9","author":"Petrovski","year":"2013","journal-title":"PLoS Genet."},{"key":"2023020110351996300_btv598-B5","doi-asserted-by":"crossref","first-page":"e33","DOI":"10.1093\/nar\/gku1322","article-title":"EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization","volume":"43","author":"Rackham","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023020110351996300_btv598-B6","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1038\/ng.3050","article-title":"A framework for the interpretation of de novo mutation in human disease","volume":"46","author":"Samocha","year":"2014","journal-title":"Nat. Genet."},{"key":"2023020110351996300_btv598-B7","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1111\/cge.12511","article-title":"The RBMX gene as a candidate for the Shashi X-linked intellectual disability syndrome","volume":"88","author":"Shashi","year":"2014","journal-title":"Clin. Genet."},{"key":"2023020110351996300_btv598-B8","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1002\/humu.22225","article-title":"Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models","volume":"34","author":"Shihab","year":"2013","journal-title":"Hum. Mutat."},{"key":"2023020110351996300_btv598-B9","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020110351996300_btv598-B10","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1093\/nar\/gkg034","article-title":"STRING: a database of predicted functional associations between proteins","volume":"31","author":"von Mering","year":"2003","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/4\/635\/49017664\/bioinformatics_32_4_635.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/4\/635\/49017664\/bioinformatics_32_4_635.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T21:58:42Z","timestamp":1675288722000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/4\/635\/1743759"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,10,21]]},"references-count":10,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2016,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv598","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,2,15]]},"published":{"date-parts":[[2015,10,21]]}}}