|
|
RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis.
Barry R Zeeberg, Hongfang Liu, Ari B Kahn, Martin Ehler, Vinodh N Rajapakse, Robert F Bonner, Jacob D Brown,
Brian P Brooks, Vladimir L Larionov, William Reinhold, John N Weinstein and Yves G Pommier.
BMC Bioinformatics 2011, 12:52doi:10.1186/1471-2105-12-52
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.
|
