{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:21:32Z","timestamp":1773271292213,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":542,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In attempts to determine the genetic causes of human disease, researchers are often faced with a large number of candidate genes. Linkage studies can point to a genomic region containing hundreds of genes, while the high-throughput sequencing approach will often identify a great number of non-synonymous genetic variants. Since systematic experimental verification of each such candidate gene is not feasible, a method is needed to decide which genes are worth investigating further. Computational gene prioritization presents itself as a solution to this problem, systematically analyzing and sorting each gene from the most to least likely to be the disease-causing gene, in a fraction of the time it would take a researcher to perform such queries manually.<\/jats:p>\n               <jats:p>Results: Here, we present Gene TIssue Expression Ranker (GeneTIER), a new web-based application for candidate gene prioritization. GeneTIER replaces knowledge-based inference traditionally used in candidate disease gene prioritization applications with experimental data from tissue-specific gene expression datasets and thus largely overcomes the bias toward the better characterized genes\/diseases that commonly afflict other methods. We show that our approach is capable of accurate candidate gene prioritization and illustrate its strengths and weaknesses using case study examples.<\/jats:p>\n               <jats:p>Availability and Implementation: Freely available on the web at http:\/\/dna.leeds.ac.uk\/GeneTIER\/.<\/jats:p>\n               <jats:p>Contact: \u00a0umaan@leeds.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv196","type":"journal-article","created":{"date-parts":[[2015,4,11]],"date-time":"2015-04-11T03:32:53Z","timestamp":1428723173000},"page":"2728-2735","source":"Crossref","is-referenced-by-count":29,"title":["GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles"],"prefix":"10.1093","volume":"31","author":[{"given":"Agne","family":"Antanaviciute","sequence":"first","affiliation":[{"name":"1 Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James\u2019s University Hospital and"}]},{"given":"Catherine","family":"Daly","sequence":"additional","affiliation":[{"name":"1 Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James\u2019s University Hospital and"}]},{"given":"Laura A.","family":"Crinnion","sequence":"additional","affiliation":[{"name":"2 Yorkshire Regional Genetics Service, St James\u2019s University Hospital, Leeds, UK"}]},{"given":"Alexander F.","family":"Markham","sequence":"additional","affiliation":[{"name":"1 Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James\u2019s University Hospital and"}]},{"given":"Christopher M.","family":"Watson","sequence":"additional","affiliation":[{"name":"2 Yorkshire Regional Genetics Service, St James\u2019s University Hospital, Leeds, UK"}]},{"given":"David T.","family":"Bonthron","sequence":"additional","affiliation":[{"name":"1 Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James\u2019s University Hospital and"}]},{"given":"Ian M.","family":"Carr","sequence":"additional","affiliation":[{"name":"1 Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James\u2019s University Hospital and"}]}],"member":"286","published-online":{"date-parts":[[2015,4,9]]},"reference":[{"issue":"Database issue","key":"2023020202214871500_btv196-B1","doi-asserted-by":"crossref","first-page":"D885","DOI":"10.1093\/nar\/gkn764","article-title":"NCBI GEO: archive for high-throughput functional genomic data","volume":"37","author":"Barrett","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020202214871500_btv196-B2","doi-asserted-by":"crossref","first-page":"3081","DOI":"10.1093\/bioinformatics\/bts581","article-title":"An 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