{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,11,14]],"date-time":"2023-11-14T20:49:48Z","timestamp":1699994988385},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Eukaryotic genes are often regulated by multiple transcription factors (TFs). Depending on the interactions among different TFs the expression of a gene can be tuned to respond to diverse environmental conditions. Chip-on-chip experiments provide a snapshot of which TF are in vivo bound to which genes in a particular condition, and have been applied to characterize the regulatory code of yeast under several experimental settings. ChIPCodis mines this data to provide new insights about how the expression of a particular group of genes is regulated. For a given list of yeast genes ChIPCodis determines which combinations of TFs are significantly over-represented in a series of environmental conditions.<\/jats:p>\n               <jats:p>Availabilty: \u00a0http:\/\/chipcodis.dacya.ucm.es<\/jats:p>\n               <jats:p>Contact: \u00a0pascual@fis.ucm.es<\/jats:p>\n               <jats:p>Supplementary information: \u00a0http:\/\/chipcodis.dacya.ucm.es\/sm.html<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn094","type":"journal-article","created":{"date-parts":[[2008,3,14]],"date-time":"2008-03-14T00:14:33Z","timestamp":1205453673000},"page":"1208-1209","source":"Crossref","is-referenced-by-count":8,"title":["ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data"],"prefix":"10.1093","volume":"24","author":[{"given":"Federico","family":"Abascal","sequence":"first","affiliation":[{"name":"1 BioComputing Unit, National Center of Biotechnology (CSIC), 2Integromics SL, Madrid and 3Computer Architecture Department. Facultad de CC F\u00edsicas. Universidad Complutense de Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pedro","family":"Carmona-Saez","sequence":"additional","affiliation":[{"name":"1 BioComputing Unit, National Center of Biotechnology (CSIC), 2Integromics SL, Madrid and 3Computer Architecture Department. Facultad de CC F\u00edsicas. Universidad Complutense de Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jose-Maria","family":"Carazo","sequence":"additional","affiliation":[{"name":"1 BioComputing Unit, National Center of Biotechnology (CSIC), 2Integromics SL, Madrid and 3Computer Architecture Department. Facultad de CC F\u00edsicas. Universidad Complutense de Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alberto","family":"Pascual-Montano","sequence":"additional","affiliation":[{"name":"1 BioComputing Unit, National Center of Biotechnology (CSIC), 2Integromics SL, Madrid and 3Computer Architecture Department. Facultad de CC F\u00edsicas. Universidad Complutense de Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,3,12]]},"reference":[{"key":"2023020210041852800_B1","doi-asserted-by":"crossref","first-page":"W186","DOI":"10.1093\/nar\/gkm323","article-title":"GeneTrail\u2013advanced gene set enrichment analysis","volume":"35","author":"Backes","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020210041852800_B2","doi-asserted-by":"crossref","first-page":"3710","DOI":"10.1093\/bioinformatics\/bth456","article-title":"GO::TermFinder\u2013open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes","volume":"20","author":"Boyle","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020210041852800_B3","doi-asserted-by":"crossref","first-page":"R3","DOI":"10.1186\/gb-2007-8-1-r3","article-title":"GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists","volume":"8","author":"Carmona-Saez","year":"2007","journal-title":"Genome Biol"},{"key":"2023020210041852800_B4","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/msb4100115","article-title":"Reconstructing dynamic regulatory maps","volume":"3","author":"Ernst","year":"2007","journal-title":"Mol. Syst. Biol"},{"key":"2023020210041852800_B5","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2002-3-11-research0059","article-title":"Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering","volume":"3","author":"Gasch","year":"2002","journal-title":"Genome Biol"},{"key":"2023020210041852800_B6","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nature02800","article-title":"Transcriptional regulatory code of a eukaryotic genome","volume":"431","author":"Harbison","year":"2004","journal-title":"Nature"},{"key":"2023020210041852800_B7","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1038\/ng2012","article-title":"Genetic reconstruction of a functional transcriptional regulatory network","volume":"39","author":"Hu","year":"2007","journal-title":"Nat. Genet"},{"key":"2023020210041852800_B8","article-title":"Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes","volume-title":"Advances in Bioinformatics and Computational Biology.","author":"Huang","year":"2006"},{"key":"2023020210041852800_B9","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1126\/science.1075090","article-title":"Transcriptional regulatory networks in Saccharomyces cerevisiae","volume":"298","author":"Lee","year":"2002","journal-title":"Science"},{"key":"2023020210041852800_B10","doi-asserted-by":"crossref","first-page":"2551","DOI":"10.1101\/gad.831000","article-title":"Orchestrated response: a symphony of transcription factors for gene control","volume":"14","author":"Lemon","year":"2000","journal-title":"Genes Dev"},{"key":"2023020210041852800_B11","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-7-113","article-title":"An improved map of conserved regulatory sites for Saccharomyces cerevisiae","volume":"7","author":"MacIsaac","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023020210041852800_B12","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/ng724","article-title":"Identifying regulatory networks by combinatorial analysis of promoter elements","volume":"29","author":"Pilpel","year":"2001","journal-title":"Nat. Genet"},{"key":"2023020210041852800_B13","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/ng1165","article-title":"Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data","volume":"34","author":"Segal","year":"2003","journal-title":"Nat. Genet"},{"key":"2023020210041852800_B14","doi-asserted-by":"crossref","first-page":"W541","DOI":"10.1093\/nar\/gkl342","article-title":"Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm","volume":"34","author":"Waleev","year":"2006","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/9\/1208\/49046752\/bioinformatics_24_9_1208.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/9\/1208\/49046752\/bioinformatics_24_9_1208.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T11:31:14Z","timestamp":1675337474000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/9\/1208\/207095"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,3,12]]},"references-count":14,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2008,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn094","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,5,1]]},"published":{"date-parts":[[2008,3,12]]}}}