RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis

Background: The Gene Ontology (GO) Consortium organizes genes into hierarchical categories based on biological process, molecular function and subcellular localization. Tools such as GoMiner can leverage GO to perform ontological analysis of microarray and proteomics studies, typically generating a list of significant functional categories. Two or more of the categories are often redundant, in the sense that identical or nearlyidentical sets of genes map to the categories. The redundancy might typically inflate the report of significant categories by a factor of three-fold, create an illusion of an overly long list of significant categories, and obscure the relevant biological interpretation. Results: We now introduce a new resource, RedundancyMiner, that de-replicates the redundant and nearlyredundant GO categories that had been determined by first running GoMiner. The main algorithm of RedundancyMiner, MultiClust, performs a novel form of cluster analysis in which a GO category migh...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Barry Zeeberg, Hongfang Liu, Ari B. Kahn, Martin Ehler, Vinodh N. Rajapakse, Robert F. Bonner, Jacob D. Brown, Brian P. Brooks, Vladimir L. Larionov, William C. Reinhold, John N. Weinstein, Yves Pommier
• Keywords: Artificial Intelligence, Biological Interpretation, BMCBI 2011, Significant Categories, Significant Functional Categories