title: RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis.
abstract: 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 nearly-identical 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 nearly-redundant 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 might belong to several category clusters. Each category cluster follows a "complete linkage" paradigm. The metric is a similarity measure that captures the overlap in gene mapping between pairs of categories.
  
  
  CONCLUSIONS
  RedundancyMiner effectively eliminated redundancies from a set of GO categories. For illustration, we have applied it to the clarification of the results arising from two current studies: (1) assessment of the gene expression profiles obtained by laser capture microdissection (LCM) of serial cryosections of the retina at the site of final optic fissure closure in the mouse embryos at specific embryonic stages, and (2) analysis of a conceptual data set obtained by examining a list of genes deemed to be "kinetochore" genes.
authors.affiliation: Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Room 5068, Building 37, 37 Convent Drive, Bethesda, MD 20892, USA. barry@discover.nci.nih.gov
authors.forename: Barry R
authors.initials: BR
authors.lastname: Zeeberg
authors.forename: Hongfang
authors.initials: H
authors.lastname: Liu
authors.forename: Ari B
authors.initials: AB
authors.lastname: Kahn
authors.forename: Martin
authors.initials: M
authors.lastname: Ehler
authors.forename: Vinodh N
authors.initials: VN
authors.lastname: Rajapakse
authors.forename: Robert F
authors.initials: RF
authors.lastname: Bonner
authors.forename: Jacob D
authors.initials: JD
authors.lastname: Brown
authors.forename: Brian P
authors.initials: BP
authors.lastname: Brooks
authors.forename: Vladimir L
authors.initials: VL
authors.lastname: Larionov
authors.forename: William
authors.initials: W
authors.lastname: Reinhold
authors.forename: John N
authors.initials: JN
authors.lastname: Weinstein
authors.forename: Yves G
authors.initials: YG
authors.lastname: Pommier
mesh_terms: D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D057225:Data Mining / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D012984:Software