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Nucleic Acids Research Advance Access first published online on April 28, 2008
This version published online on May 22, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn215
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© 2008 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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CoPub: a literature-based keyword enrichment tool for microarray data analysis

Raoul Frijters1, Bart Heupers2, Pieter van Beek2, Maurice Bouwhuis2, René van Schaik3, Jacob de Vlieg1,3, Jan Polman3 and Wynand Alkema3,*

1Computational Drug Discovery (CDD),, Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University Nijmegen Medical Centre, Nijmegen, 2SARA Computing and Network Services, Amsterdam and 3Department of Molecular Design & Informatics, Organon, part of Schering-Plough Corporation, Oss, The Netherlands

*To whom correspondence should be addressed. Tel: +31 (0)412 663678; Fax: +31 (0)412 662553; Email: wynand.alkema{at}organon.com

Received January 30, 2008. Revised April 4, 2008. Accepted April 9, 2008.

Medline is a rich information source, from which links between genes and keywords describing biological processes, pathways, drugs, pathologies and diseases can be extracted. We developed a publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. CoPub is freely accessible at http://services.nbic.nl/cgi-bin/copub/CoPub.pl.


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