{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:36Z","timestamp":1740185136298,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2022,9,20]],"date-time":"2022-09-20T00:00:00Z","timestamp":1663632000000},"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\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2019R1A5A2026045","NRF-2017M3A9B6061509"],"award-info":[{"award-number":["NRF-2019R1A5A2026045","NRF-2017M3A9B6061509"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Korea Health Technology R&D Project"},{"DOI":"10.13039\/501100003710","name":"Korea Health Industry Development Institute","doi-asserted-by":"publisher","award":["HR21C1003"],"award-info":[{"award-number":["HR21C1003"]}],"id":[{"id":"10.13039\/501100003710","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Multi-omic profiling data, such as The Cancer Genome Atlas and pharmacogenomic data, facilitate research into cancer mechanisms and drug development. However, it is not easy for researchers to connect, integrate and analyze huge and heterogeneous data, which is a major obstacle to the utilization of cancer genomic data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed Cancer Genome Viewer (CGV), a user-friendly web service that provides functions to integrate and visualize cancer genome data and pharmacogenomic data. Users can easily select and customize the samples to be analyzed with the pre-defined selection options for patients\u2019 clinic-pathological features from multiple datasets. Using the customized dataset, users can perform subsequent data analyses comprehensively, including gene set analysis, clustering or survival analysis. CGV also provides pre-calculated drug response scores from pharmacogenomic data, which may facilitate the discovery of new cancer targets and therapeutics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CGV web service is implemented with the R Shiny application at http:\/\/cgv.sysmed.kr and the source code is freely available at https:\/\/git.sysmed.kr\/sysmed_public\/cgv.<\/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\/btac642","type":"journal-article","created":{"date-parts":[[2022,9,21]],"date-time":"2022-09-21T18:43:39Z","timestamp":1663785819000},"page":"5116-5118","source":"Crossref","is-referenced-by-count":0,"title":["CGV: Cancer Genome Viewer, a web service for integrative cancer genome and pharmacogenomic data analysis"],"prefix":"10.1093","volume":"38","author":[{"given":"Ji-Hye","family":"Choi","sequence":"first","affiliation":[{"name":"Department of Physiology, Ajou University School of Medicine , Suwon 16499, Republic of Korea"},{"name":"Department of Biomedical Science, Graduate School, Ajou University , Suwon 16499, Republic of Korea"}]},{"given":"Hui-Seon","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Physiology, Ajou University School of Medicine , Suwon 16499, Republic of Korea"},{"name":"Department of Biomedical Science, Graduate School, Ajou University , Suwon 16499, Republic of Korea"}]},{"given":"Seong-Ho","family":"Cho","sequence":"additional","affiliation":[{"name":"Department of Physiology, Ajou University School of Medicine , Suwon 16499, Republic of Korea"}]},{"given":"Ji-Hye","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Physiology, Ajou University School of Medicine , Suwon 16499, Republic of Korea"},{"name":"Department of Biomedical Science, Graduate School, Ajou University , Suwon 16499, Republic of Korea"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0916-893X","authenticated-orcid":false,"given":"Hyun Goo","family":"Woo","sequence":"additional","affiliation":[{"name":"Department of Physiology, Ajou University School of Medicine , Suwon 16499, Republic of Korea"},{"name":"Department of Biomedical Science, Graduate School, Ajou University , Suwon 16499, Republic of Korea"}]}],"member":"286","published-online":{"date-parts":[[2022,9,20]]},"reference":[{"key":"2022112014194550600_btac642-B1","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"2022112014194550600_btac642-B2","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1158\/2159-8290.CD-12-0095","article-title":"The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data","volume":"2","author":"Cerami","year":"2012","journal-title":"Cancer Discov"},{"key":"2022112014194550600_btac642-B3","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.neo.2022.01.001","article-title":"UALCAN: an update to the integrated cancer data analysis platform","volume":"25","author":"Chandrashekar","year":"2022","journal-title":"Neoplasia"},{"key":"2022112014194550600_btac642-B4","doi-asserted-by":"crossref","first-page":"e71","DOI":"10.1093\/nar\/gkv1507","article-title":"TCGAbiolinks: an R\/bioconductor package for integrative analysis of TCGA data","volume":"44","author":"Colaprico","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2022112014194550600_btac642-B5","doi-asserted-by":"crossref","first-page":"e107468","DOI":"10.1371\/journal.pone.0107468","article-title":"pRRophetic: an R package for prediction of clinical chemotherapeutic response from tumor gene expression levels","volume":"9","author":"Geeleher","year":"2014","journal-title":"PLoS One"},{"key":"2022112014194550600_btac642-B6","doi-asserted-by":"crossref","first-page":"885","DOI":"10.3390\/cancers13040885","article-title":"Facilitating drug discovery in breast cancer by virtually screening patients using in vitro drug response modeling","volume":"13","author":"Gruener","year":"2021","journal-title":"Cancers (Basel)"},{"key":"2022112014194550600_btac642-B7","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1093\/biostatistics\/kxj037","article-title":"Adjusting batch effects in microarray expression data using empirical Bayes methods","volume":"8","author":"Johnson","year":"2007","journal-title":"Biostatistics"},{"key":"2022112014194550600_btac642-B8","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"Liberzon","year":"2011","journal-title":"Bioinformatics"},{"key":"2022112014194550600_btac642-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":"2022112014194550600_btac642-B10","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1016\/j.mayocp.2017.09.001","article-title":"Pharmacogenomics: precision medicine and drug response","volume":"92","author":"Weinshilboum","year":"2017","journal-title":"Mayo Clin. Proc"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac642\/46129055\/btac642.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/22\/5116\/47153851\/btac642.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/22\/5116\/47153851\/btac642.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,20]],"date-time":"2022-11-20T14:20:00Z","timestamp":1668954000000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/22\/5116\/6706784"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,9,20]]},"references-count":10,"journal-issue":{"issue":"22","published-online":{"date-parts":[[2022,9,20]]},"published-print":{"date-parts":[[2022,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac642","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2022,11,15]]},"published":{"date-parts":[[2022,9,20]]}}}