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

• Published in: Nucleic acids research Vol. 36; no. suppl-2; pp. W406 - W410
• Main Authors: Frijters, Raoul, Heupers, Bart, van Beek, Pieter, Bouwhuis, Maurice, van Schaik, René, de Vlieg, Jacob, Polman, Jan, Alkema, Wynand
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-07-2008; Oxford Publishing Limited (England)
• Subjects: Animals; Gene Expression Profiling; Humans; Internet; MEDLINE; Mice; Oligonucleotide Array Sequence Analysis; Rats; Software; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkn215

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.