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Nucleic Acids Research Advance Access originally published online on May 22, 2009
Nucleic Acids Research 2009 37(Web Server issue):W317-W322; doi:10.1093/nar/gkp416
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W317-W322
© 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.

Articles

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information

Ruben Nogales-Cadenas1, Pedro Carmona-Saez1, Miguel Vazquez2, Cesar Vicente1, Xiaoyuan Yang1, Francisco Tirado1, Jose María Carazo3 and Alberto Pascual-Montano1,*

1Computer Architecture Department, 2Software Engineering Department, Complutense University of Madrid and 3Biocomputing Unit, National Center for Biotechnology, CNB-CSIC, Madrid, Spain

*To whom correspondence should be addressed. Tel: +34 913944420; Fax: +34 913944687; Email: pascual{at}fis.ucm.es 

Received January 31, 2009. Revised April 24, 2009. Accepted May 6, 2009.

GeneCodis is a web server application for functional analysis of gene lists that integrates different sources of information and finds modular patterns of interrelated annotations. This integrative approach has proved to be useful for the interpretation of high-throughput experiments and therefore a new version of the system has been developed to expand its functionality and scope. GeneCodis now expands the functional information with regulatory patterns and user-defined annotations, offering the possibility of integrating all sources of information in the same analysis. Traditional singular enrichment is now permitted and more organisms and gene identifiers have been added to the database. The application has been re-engineered to improve performance, accessibility and scalability. In addition, GeneCodis can now be accessed through a public SOAP web services interface, enabling users to perform analysis from their own scripts and workflows. The application is freely available at http://genecodis.dacya.ucm.es


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