Gene List significance at-a-glance with GeneValorization.

Bryan Brancotte Anne Biton Isabelle Bernard-Pierrot François Radvanyi 1 Fabien Reyal Sarah Cohen-Boulakia 2, 3
1 CDC - Compartimentation et dynamique cellulaires
2 LRI - Laboratoire de Recherche en Informatique
3 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : 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. 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. AVAILABILITY: http://bioguide-project.net/gv CONTACT: cohen@lri.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Journal articles
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https://hal.inria.fr/inria-00627865
Contributor : Sarah Cohen-Boulakia <>
Submitted on : Thursday, September 29, 2011 - 5:01:03 PM
Last modification on : Wednesday, July 10, 2019 - 7:14:02 PM

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INRIA | LIX | PARISTECH | X | X-LIX | CURIE | FNCLCC | UMR8623 | UMR144 | UPMC | PSL | X-DEP-INFO | SORBONNE-UNIVERSITE | SU-SCIENCES

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Bryan Brancotte, Anne Biton, Isabelle Bernard-Pierrot, François Radvanyi, Fabien Reyal, et al.. Gene List significance at-a-glance with GeneValorization.. Bioinformatics, Oxford University Press (OUP), 2011, 27 (8), pp.1187-9. ⟨10.1093/bioinformatics/btr073⟩. ⟨inria-00627865⟩

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