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CoPub: a literature-based keyword enrichment tool for microarray data analysis.

Frijters R, Heupers B, Beek PV, Bouwhuis M, Schaik RV, Vlieg JD, Polman J, Alkema W

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

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.

Published 29 April 2008 in Nucleic Acids Res.
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