{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:53Z","timestamp":1740185153285,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,3,1]],"date-time":"2018-03-01T00:00:00Z","timestamp":1519862400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000050","name":"NHLBI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Programs of Excellence in Glycosciences","award":["HL107152"],"award-info":[{"award-number":["HL107152"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Although RNA expression data are accumulating at a remarkable speed, gaining insights from them still requires laborious analyses, which hinder many biological and biomedical researchers. This report introduces a visual analytics framework that applies several well-known visualization techniques to leverage understanding of an RNA expression dataset. Our analyses on glycosaminoglycan-related genes have demonstrated the broad application of this tool, anexVis (analysis of RNA expression), to advance the understanding of tissue-specific glycosaminoglycan regulation and functions, and potentially other biological pathways.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The application is accessible at https:\/\/anexvis.chpc.utah.edu\/, source codes deposited on GitHub.<\/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\/bty122","type":"journal-article","created":{"date-parts":[[2018,3,1]],"date-time":"2018-03-01T04:11:38Z","timestamp":1519877498000},"page":"2510-2512","source":"Crossref","is-referenced-by-count":1,"title":["anexVis: visual analytics framework for analysis of RNA expression"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4219-2990","authenticated-orcid":false,"given":"Diem-Trang","family":"Tran","sequence":"first","affiliation":[{"name":"Department of Medicinal Chemistry"},{"name":"School of Computing, University of Utah, Salt Lake City, UT, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tian","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computing, University of Utah, Salt Lake City, UT, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryan","family":"Stutsman","sequence":"additional","affiliation":[{"name":"School of Computing, University of Utah, Salt Lake City, UT, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Might","sequence":"additional","affiliation":[{"name":"Hugh Kaul Personalized Medicine Institute, University of Alabama at Birmingham, Birmingham, AL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Umesh R","family":"Desai","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Balagurunathan","family":"Kuberan","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry"},{"name":"Department of Biology, University of Utah, Salt Lake City, UT, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,3,1]]},"reference":[{"key":"2023012713015390000_bty122-B2","doi-asserted-by":"crossref","first-page":"e23","DOI":"10.1158\/0008-5472.CAN-17-0318","article-title":"A galaxy implementation of next-generation clustered heatmaps for interactive exploration of molecular profiling data","volume":"77","author":"Broom","year":"2017","journal-title":"Cancer Res"},{"key":"2023012713015390000_bty122-B3","doi-asserted-by":"crossref","first-page":"3123","DOI":"10.1093\/bioinformatics\/btx337","article-title":"ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data","volume":"33","author":"Gardeux","year":"2017","journal-title":"Bioinformatics"},{"key":"2023012713015390000_bty122-B4","doi-asserted-by":"crossref","first-page":"47.","DOI":"10.1186\/s12864-016-3396-5","article-title":"DEIVA: a web application for interactive visual analysis of differential gene expression profiles","volume":"18","author":"Harshbarger","year":"2017","journal-title":"BMC Genomics"},{"key":"2023012713015390000_bty122-B5","doi-asserted-by":"crossref","first-page":"e0176334.","DOI":"10.1371\/journal.pone.0176334","article-title":"Shinyheatmap: ultra fast low memory heatmap web interface for big data genomics","volume":"12","author":"Khomtchouk","year":"2017","journal-title":"PLos One"},{"key":"2023012713015390000_bty122-B6","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1126\/science.aaa0355","article-title":"The human transcriptome across tissues and individuals","volume":"348","author":"Mel\u00e9","year":"2015","journal-title":"Science"},{"year":"2014","author":"Ooms","key":"2023012713015390000_bty122-B7"},{"key":"2023012713015390000_bty122-B8","first-page":"314","article-title":"Toil enables reproducible, open source, big biomedical data analyses","volume-title":"Nat. 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