{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T15:10:58Z","timestamp":1714749058013},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: BioCichlid is a 3D visualization system of time-course microarray data on molecular networks, aiming at interpretation of gene expression data by transcriptional relationships based on the central dogma with physical and genetic interactions. BioCichlid visualizes both physical (protein) and genetic (regulatory) network layers, and provides animation of time-course gene expression data on the genetic network layer. Transcriptional regulations are represented to bridge the physical network (transcription factors) and genetic network (regulated genes) layers, thus integrating promoter analysis into the pathway mapping. BioCichlid enhances the interpretation of microarray data and allows for revealing the underlying mechanisms causing differential gene expressions.<\/jats:p>\n               <jats:p>Availability: BioCichlid is freely available and can be accessed at http:\/\/newton.tmd.ac.jp\/. Source codes for both biocichlid server and client are also available.<\/jats:p>\n               <jats:p>Contact: \u00a0ogishima@bioinfo.tmd.ac.jp<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp008","type":"journal-article","created":{"date-parts":[[2009,1,7]],"date-time":"2009-01-07T02:49:37Z","timestamp":1231296577000},"page":"543-544","source":"Crossref","is-referenced-by-count":6,"title":["BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network"],"prefix":"10.1093","volume":"25","author":[{"given":"Ryosuke R.","family":"Ishiwata","sequence":"first","affiliation":[{"name":"1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masaki S.","family":"Morioka","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Soichi","family":"Ogishima","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroshi","family":"Tanaka","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan"},{"name":"1 Department of Computational Biology, School of Medical Sciences and 2Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,1,6]]},"reference":[{"key":"2023013110115082900_B1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/ng0502-19","article-title":"GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways","volume":"31","author":"Dahlquist","year":"2002","journal-title":"Nat. Genet."},{"key":"2023013110115082900_B2","first-page":"179","article-title":"GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks","volume":"8","author":"Vlasblom","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013110115082900_B3","first-page":"2178","article-title":"Genome Expression Pathway Analysis Tool \u2013 analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context","volume":"22","author":"Weniger","year":"2007","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/543\/48985593\/bioinformatics_25_4_543.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/543\/48985593\/bioinformatics_25_4_543.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:28:25Z","timestamp":1675189705000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/4\/543\/250900"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1,6]]},"references-count":3,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2009,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp008","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,2,15]]},"published":{"date-parts":[[2009,1,6]]}}}