{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T10:52:39Z","timestamp":1740135159074,"version":"3.37.3"},"reference-count":17,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,3,22]],"date-time":"2016-03-22T00:00:00Z","timestamp":1458604800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,3,22]],"date-time":"2016-03-22T00:00:00Z","timestamp":1458604800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["Intramural Research Program"],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"Abstract<\/jats:title>\n Background<\/jats:title>\n Translational genomics research in cancers, e.g., International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), has generated large multidimensional datasets from high-throughput technologies. Data analysis at multidimensional level will greatly benefit clinical applications of genomic information in diagnosis, prognosis and therapeutics of cancers. To help, tools to effectively visualize integrated multidimensional data are important for understanding and describing the relationship between genomic variations and cancers.<\/jats:p>\n <\/jats:sec>\n Results<\/jats:title>\n We implemented the R package, caOmicsV, to provide methods under R environment to visualize multidimensional cancer genomic data in two layouts: matrix layout and combined biological network and circular layout. Both layouts support to display sample information, gene expression (e.g., RNA and miRNA), DNA methylation, DNA copy number variations, and summarized data. A set of supplemental functions are included in the caOmicsV package to help users in generation of plot data sets from multiple genomic datasets with given gene names and sample names. Default plot methods for both layouts for easy use are also implemented.<\/jats:p>\n <\/jats:sec>\n Conclusion<\/jats:title>\n caOmicsV package provides an easy and flexible way to visualize integrated multidimensional cancer genomic data under R environment.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/s12859-016-0989-6","type":"journal-article","created":{"date-parts":[[2016,3,22]],"date-time":"2016-03-22T13:02:19Z","timestamp":1458651739000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["caOmicsV: an R package for visualizing multidimensional cancer genomic data"],"prefix":"10.1186","volume":"17","author":[{"given":"Hongen","family":"Zhang","sequence":"first","affiliation":[]},{"given":"Paul S.","family":"Meltzer","sequence":"additional","affiliation":[]},{"given":"Sean R.","family":"Davis","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,3,22]]},"reference":[{"key":"989_CR1","unstructured":"The Cancer Genome Atlas (TCGA). http:\/\/cancergenome.nih.gov\/. Accessed 2 May 2015."},{"key":"989_CR2","unstructured":"International Cancer Genome Consortium. https:\/\/icgc.org\/. Accessed 2 May 2015."},{"key":"989_CR3","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1038\/nmeth.1422","volume":"7","author":"CB Nielsen","year":"2010","unstructured":"Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T. Visualizing genomes: techniques and challenges. Nat Methods. 2010;7:S5\u2013S15.","journal-title":"Nat Methods"},{"key":"989_CR4","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/gm413","volume":"5","author":"MP Schroeder","year":"2013","unstructured":"Schroeder MP, Gonzalez-Perez A, Lopez-Bigas N. Visualizing multidimensional cancer genomics data. Genome Med. 2013;5:9.","journal-title":"Genome Med"},{"key":"989_CR5","doi-asserted-by":"publisher","first-page":"1356","DOI":"10.1002\/pmic.201400377","volume":"15","author":"R Wang","year":"2015","unstructured":"Wang R, Perez-Riverol Y, Hermjakob H, Vizca\u00edno JA. Open source libraries and frameworks for biological data visualisation: A guide for developers. Proteomics. 2015;15:1356\u201374.","journal-title":"Proteomics"},{"key":"989_CR6","unstructured":"The UCSC Cancer Genomics Browser. https:\/\/genome-cancer.ucsc.edu. Accessed 2 May 2015."},{"issue":"2","key":"989_CR7","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1093\/bib\/bbs017","volume":"14","author":"H Thorvaldsd\u00f3ttir","year":"2013","unstructured":"Thorvaldsd\u00f3ttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178\u201392.","journal-title":"Brief Bioinform"},{"key":"989_CR8","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1101\/gr.092759.109","volume":"19","author":"M Krzywinski","year":"2009","unstructured":"Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639\u201345.","journal-title":"Genome Res"},{"key":"989_CR9","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1186\/1471-2105-14-244","volume":"14","author":"H Zhang","year":"2013","unstructured":"Zhang H, Davis S, Meltzer PS. RCircos: an R package for Circos 2D track plots. BMC Bioinform. 2013;14:244.","journal-title":"BMC Bioinform"},{"key":"989_CR10","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1093\/bioinformatics\/btu842","volume":"31","author":"J An","year":"2015","unstructured":"An J, Lai J, Sajjanhar A, Batra J, Wang C, Nelson CC. J-Circos: an interactive Circos plotte. Bioinformatics. 2015;31:1463\u20135.","journal-title":"Bioinformatics"},{"key":"989_CR11","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1158\/2159-8290.CD-12-0095","volume":"2","author":"E Cerami","year":"2012","unstructured":"Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N. The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data. Cancer Disco. 2012;2:401\u20134.","journal-title":"Cancer Disco."},{"key":"989_CR12","doi-asserted-by":"publisher","first-page":"i237","DOI":"10.1093\/bioinformatics\/btq182","volume":"26","author":"CJ Vaske","year":"2010","unstructured":"Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 2010;26:i237\u201345.","journal-title":"Bioinformatics"},{"key":"989_CR13","doi-asserted-by":"publisher","first-page":"W218","DOI":"10.1093\/nar\/gkt473","volume":"41","author":"CK Wong","year":"2013","unstructured":"Wong CK, Vaske CJ, Ng S, Zachary Sanborn J, Ben S, Haussler D, Stuart JM. The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Res. 2013;41:W218\u201324.","journal-title":"Nucleic Acids Res."},{"key":"989_CR14","doi-asserted-by":"publisher","first-page":"R77","DOI":"10.1186\/gb-2012-13-8-r77","volume":"13","author":"T Yin","year":"2012","unstructured":"Yin T, Cook D, Lawrence M. ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biology. 2012;13:R77.","journal-title":"Genome Biology"},{"key":"989_CR15","doi-asserted-by":"publisher","first-page":"2811","DOI":"10.1093\/bioinformatics\/btu393","volume":"30","author":"Z Gu","year":"2014","unstructured":"Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics. 2014;30:2811\u20132.","journal-title":"Bioinformatics"},{"key":"989_CR16","doi-asserted-by":"publisher","first-page":"13","DOI":"10.4137\/CIN.S13495","volume":"13","author":"Y Hu","year":"2014","unstructured":"Hu Y, Yan C, Hsu CH, Chen QR, Niu K, Komatsoulis GA, Meerzaman D. OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data. Cancer Inform. 2014;13:13\u201320.","journal-title":"Cancer Inform"},{"key":"989_CR17","unstructured":"Gu Z. ComplexHeatmap: Making Complex Heatmaps. R package version 1.0.0, https:\/\/github.com\/jokergoo\/ComplexHeatmap. Accessed 2 May 2015."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-0989-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-016-0989-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-0989-6","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-0989-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:01:28Z","timestamp":1706810488000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-0989-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,3,22]]},"references-count":17,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["989"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-0989-6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2016,3,22]]},"assertion":[{"value":"18 November 2015","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 March 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 March 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"141"}}