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Nucleic Acids Research Advance Access published online on April 30, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp263
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis

Daniel Glez-Peña1, Gonzalo Gómez-López2, David G. Pisano2 and Florentino Fdez-Riverola1,3,*

1Higher Technical School of Computer Engineering, University of Vigo, Ourense, 2Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid and 3Informatics Department, University of Vigo, Vigo, Pontevedra, Spain

*To whom correspondence should be addressed. Tel: +34 988 387015; Fax: +34 988 387001; Email: riverola{at}uvigo.es

Received January 30, 2009. Revised April 3, 2009. Accepted April 8, 2009.

WhichGenes is a web-based interactive gene set building tool offering a very simple interface to extract always-updated gene lists from multiple databases and unstructured biological data sources. While the user can specify new gene sets of interest by following a simple four-step wizard, the tool is able to run several queries in parallel. Every time a new set is generated, it is automatically added to the private gene-set cart and the user is notified by an e-mail containing a direct link to the new set stored in the server. WhichGenes provides functionalities to edit, delete and rename existing sets as well as the capability of generating new ones by combining previous existing sets (intersection, union and difference operators). The user can export his sets configuring the output format and selecting among multiple gene identifiers. In addition to the user-friendly environment, WhichGenes allows programmers to access its functionalities in a programmatic way through a Representational State Transfer web service. WhichGenes front-end is freely available at http://www.whichgenes.org/, WhichGenes API is accessible at http://www.whichgenes.org/api/.


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