{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T21:42:15Z","timestamp":1722980535800},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2048,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput technologies provide fundamental informations concerning thousands of genes. Many of the current research laboratories daily use one or more of these technologies and end-up with lists of genes. Assessing the originality of the results obtained includes being aware of the number of publications available concerning individual or multiple genes and accessing information about these publications. Faced with the exponential growth of publications avaliable and number of genes involved in a study, this task is becoming particularly difficult to achieve.<\/jats:p>\n               <jats:p>Results: We introduce GeneValorization, a web-based tool that gives a clear and handful overview of the bibliography available corresponding to the user input formed by (i) a gene list (expressed by gene names or ids from EntrezGene) and (ii) a context of study (expressed by keywords). From this input, GeneValorization provides a matrix containing the number of publications with co-occurrences of gene names and keywords. Graphics are automatically generated to assess the relative importance of genes within various contexts. Links to publications and other databases offering information on genes and keywords are also available. To illustrate how helpful GeneValorization is, we will consider the gene list of the OncotypeDX prognostic marker test.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/bioguide-project.net\/gv<\/jats:p>\n               <jats:p>Contact: \u00a0cohen@lri.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr073","type":"journal-article","created":{"date-parts":[[2011,2,25]],"date-time":"2011-02-25T01:38:20Z","timestamp":1298597900000},"page":"1187-1189","source":"Crossref","is-referenced-by-count":13,"title":["Gene List significance at-a-glance with GeneValorization"],"prefix":"10.1093","volume":"27","author":[{"given":"Bryan","family":"Brancotte","sequence":"first","affiliation":[{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"}]},{"given":"Anne","family":"Biton","sequence":"additional","affiliation":[{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"},{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"},{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"},{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"}]},{"given":"Isabelle","family":"Bernard-Pierrot","sequence":"additional","affiliation":[{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"},{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"}]},{"given":"Fran\u00e7ois","family":"Radvanyi","sequence":"additional","affiliation":[{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"},{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"}]},{"given":"Fabien","family":"Reyal","sequence":"additional","affiliation":[{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"},{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"},{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"}]},{"given":"Sarah","family":"Cohen-Boulakia","sequence":"additional","affiliation":[{"name":"1 Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universit\u00e9 Paris-Sud, F\u221291405 Orsay Cedex, 2CNRS, UMR 144, Institut Curie, 26 rue d'Ulm, F-75248 Paris Cedex 05, 3Institut Curie, Centre de Recherche, Paris, F-75248, 4INSERM, U900, Paris, F\u221275248, 5Mines ParisTech, Fontainebleau, F\u221277300 and 6Institut Curie, Departement de Chirurgie, 6 rue d'Ulm, F-75005 Paris, France"}]}],"member":"286","published-online":{"date-parts":[[2011,2,23]]},"reference":[{"key":"2023061312070998800_B1","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/1471-2105-6-51","article-title":"CoPub Mapper: mining MEDLINE based on search term co-publication","volume":"6","author":"Alako","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023061312070998800_B2","doi-asserted-by":"crossref","first-page":"2055","DOI":"10.1093\/bioinformatics\/btl342","article-title":"PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature","volume":"22","author":"Grimes","year":"2006","journal-title":"Bioinformatics"},{"issue":"Suppl. 2","key":"2023061312070998800_B3","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1186\/gb-2008-9-s2-s8","article-title":"Linking genes to literature: text mining, information extraction, and retrieval applications for biology","volume":"9","author":"Krallinger","year":"2008","journal-title":"Genome Biol."},{"key":"2023061312070998800_B4","doi-asserted-by":"crossref","first-page":"2817","DOI":"10.1056\/NEJMoa041588","article-title":"A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer","volume":"351","author":"Paik","year":"2004","journal-title":"N. Engl. J. Med."},{"key":"2023061312070998800_B5","doi-asserted-by":"crossref","first-page":"W300","DOI":"10.1093\/nar\/gkp429","article-title":"GoGene: gene annotation in the fast lane","volume":"37","author":"Plake","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023061312070998800_B6","doi-asserted-by":"crossref","first-page":"366","DOI":"10.2174\/1871526510909030366","article-title":"Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMed","volume":"3","author":"Vellay","year":"2009","journal-title":"Infect. 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