{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:18:20Z","timestamp":1761862700427,"version":"3.33.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: One of the most challenging tasks in the post-genomic era is the reconstruction of transcriptional regulation networks. The goal is to identify, for each gene expressed in a particular cellular context, the regulators affecting its transcription, and the co-ordination of several regulators in specific types of regulation. DNA microarrays can be used to investigate relationships between regulators and their target genes, through simultaneous observations of their RNA levels.<\/jats:p><jats:p>Results: We propose a data mining system for inferring transcriptional regulation relationships from RNA expression values. This system is particularly suitable for the detection of cooperative transcriptional regulation. We model regulatory relationships as labelled two-layer gene regulatory networks, and describe a method for the efficient learning of these bipartite networks from discretized expression data sets. We also evaluate the statistical significance of such inferred networks and validate our methods on two public yeast expression data sets.<\/jats:p><jats:p>Availability: \u00a0http:\/\/www.lri.fr\/~elati\/licorn.html<\/jats:p><jats:p>Contact: \u00a0mohamed.elati@curie.fr<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm352","type":"journal-article","created":{"date-parts":[[2007,8,25]],"date-time":"2007-08-25T00:30:08Z","timestamp":1188001808000},"page":"2407-2414","source":"Crossref","is-referenced-by-count":40,"title":["LICORN: learning cooperative regulation networks from gene expression data"],"prefix":"10.1093","volume":"23","author":[{"given":"Mohamed","family":"Elati","sequence":"first","affiliation":[{"name":"1 LRI, CNRS UMR 8623, b\u00e2t 490, Universit\u00e9 Paris Sud, 91405 F-Orsay, 2Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75248 F-Paris, 3Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, 75248 F-Paris and 4IGM, CNRS UMR 8621, b\u00e2t 400\/409, Universit\u00e9 Paris-Sud, 91405 F-Orsay, France"},{"name":"1 LRI, CNRS UMR 8623, b\u00e2t 490, Universit\u00e9 Paris Sud, 91405 F-Orsay, 2Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75248 F-Paris, 3Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, 75248 F-Paris and 4IGM, CNRS UMR 8621, b\u00e2t 400\/409, Universit\u00e9 Paris-Sud, 91405 F-Orsay, France"}]},{"given":"Pierre","family":"Neuvial","sequence":"additional","affiliation":[{"name":"1 LRI, CNRS UMR 8623, b\u00e2t 490, Universit\u00e9 Paris Sud, 91405 F-Orsay, 2Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75248 F-Paris, 3Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, 75248 F-Paris and 4IGM, CNRS UMR 8621, b\u00e2t 400\/409, Universit\u00e9 Paris-Sud, 91405 F-Orsay, France"}]},{"given":"Monique","family":"Bolotin-Fukuhara","sequence":"additional","affiliation":[{"name":"1 LRI, CNRS UMR 8623, b\u00e2t 490, Universit\u00e9 Paris Sud, 91405 F-Orsay, 2Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75248 F-Paris, 3Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, 75248 F-Paris and 4IGM, CNRS UMR 8621, b\u00e2t 400\/409, Universit\u00e9 Paris-Sud, 91405 F-Orsay, France"}]},{"given":"Emmanuel","family":"Barillot","sequence":"additional","affiliation":[{"name":"1 LRI, CNRS UMR 8623, b\u00e2t 490, Universit\u00e9 Paris Sud, 91405 F-Orsay, 2Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75248 F-Paris, 3Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, 75248 F-Paris and 4IGM, CNRS UMR 8621, b\u00e2t 400\/409, Universit\u00e9 Paris-Sud, 91405 F-Orsay, France"}]},{"given":"Fran\u00e7ois","family":"Radvanyi","sequence":"additional","affiliation":[{"name":"1 LRI, CNRS UMR 8623, b\u00e2t 490, Universit\u00e9 Paris Sud, 91405 F-Orsay, 2Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75248 F-Paris, 3Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, 75248 F-Paris and 4IGM, CNRS UMR 8621, b\u00e2t 400\/409, Universit\u00e9 Paris-Sud, 91405 F-Orsay, France"}]},{"given":"C\u00e9line","family":"Rouveirol","sequence":"additional","affiliation":[{"name":"1 LRI, CNRS UMR 8623, b\u00e2t 490, Universit\u00e9 Paris Sud, 91405 F-Orsay, 2Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75248 F-Paris, 3Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, 75248 F-Paris and 4IGM, CNRS UMR 8621, b\u00e2t 400\/409, Universit\u00e9 Paris-Sud, 91405 F-Orsay, France"}]}],"member":"286","published-online":{"date-parts":[[2007,9,15]]},"reference":[{"key":"2023041106230447400_","first-page":"207","article-title":"Mining association rules between sets of items in large databases","author":"Agrawal","year":"1993"},{"key":"2023041106230447400_","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/j.jmb.2006.04.026","article-title":"Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast","volume":"360","author":"Balaji","year":"2006","journal-title":"J. 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