{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T18:28:07Z","timestamp":1747852087978,"version":"3.37.3"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2018,10,10]],"date-time":"2018-10-10T00:00:00Z","timestamp":1539129600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100007579","name":"Auburn University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007579","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Predicting genetic regulatory variants, most of which locate in non-coding genomic regions, still remain a challenge in genetic research. Among all non-coding regulatory variants, cis-eQTL single nucleotide variants (SNVs) are of particular interest for their crucial role in regulating gene expression. Since different gene expression patterns are believed to contribute to the etiologies of different phenotypes, it is desirable to characterize the impact of cis-eQTL SNVs in a context-specific manner. Though computational methods for predicting the potential of variants being pathogenic or deleterious are well-established, methods for annotating and predicting cis-eQTL SNVs are under-developed. Here, we present TIVAN (TIssue-specific Variant ANnotation and prediction), an ensemble method of decision trees, to predict tissue-specific cis-eQTL SNVs. TIVAN is trained based on a comprehensive collection of features, including genome-wide genomic and epigenomic profiling data. As a result, TIVAN has been shown to accurately discriminate cis-eQTL SNVs from non-eQTL SNVs and perform favorably to other methods by obtaining higher five-fold cross-validation AUC values (CV-AUC) and Leave-One-Chromosome-Out predicted AUC values (LOCO-AUC) across 44 different tissues belonging to 27 different tissue classes. Finally, TIVAN consistently maintains top performance on an independent testing dataset, which includes 7 tissues in 11 studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TIVAN software is available at https:\/\/github.com\/lichen-lab\/TIVAN.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty872","type":"journal-article","created":{"date-parts":[[2018,10,9]],"date-time":"2018-10-09T19:34:48Z","timestamp":1539113688000},"page":"1573-1575","source":"Crossref","is-referenced-by-count":17,"title":["TIVAN: tissue-specific <i>cis<\/i>-eQTL single nucleotide variant annotation and prediction"],"prefix":"10.1093","volume":"35","author":[{"given":"Li","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Health Outcomes Research and Policy, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA"},{"name":"Department of Computer Science and Software Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, AL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ye","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Software Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, AL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bing","family":"Yao","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amit","family":"Mitra","sequence":"additional","affiliation":[{"name":"Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xu","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA"},{"name":"HudsonAlpha Institute for Biotechnology, Huntsville, AL"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao","family":"Qin","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Software Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, AL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,10,10]]},"reference":[{"key":"2023012806493410800_bty872-B1","doi-asserted-by":"crossref","first-page":"e1003649","DOI":"10.1371\/journal.pgen.1003649","article-title":"Integrative modeling of eqtls and cis-regulatory elements suggests mechanisms underlying cell type specificity of eqtls","volume":"9","author":"Brown","year":"2013","journal-title":"PLoS Genet"},{"key":"2023012806493410800_bty872-B2","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1186\/s13059-016-1112-z","article-title":"Divan: accurate identification of non-coding disease-specific risk variants using multi-omics profiles","volume":"17","author":"Chen","year":"2016","journal-title":"Genome Biol."},{"key":"2023012806493410800_bty872-B3","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1186\/s13104-017-2851-y","article-title":"Using divan to assess disease\/trait-associated single nucleotide variants in genome-wide scale","volume":"10","author":"Chen","year":"2017","journal-title":"BMC Res. 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