Functional profiling of microarray experiments using text-mining derived bioentities

Motivation: The increasing use of microarray technologies brought about a parallel demand in methods for the functional interpretation of the results. Beyond the conventional functional annotations for genes, such as gene ontology, pathways, etc. other sources of information are still to be exploited. Text-mining methods allow extracting informative terms (bioentities) with different functional, chemical, clinical, etc. meanings, that can be associated to genes. We show how to use these associations within an appropriate statistical framework and how to apply them through easy-to-use, web-based environments to the functional interpretation of microarray experiments. Functional enrichment and gene set enrichment tests using bioentities are presented. Availability: Marmite and MarmiteScan can be found in the Babelomics suite: http://www.babelomics.org Contact: jdopazo@cipf.es Supplementary information: Supplementary data are available at Bioinformatics online.