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IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov 15. [Epub ahead of print]

A New Path Based Hybrid Measure for Gene Ontology Similarity.

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1
Indian Statistical Institute, Kolkata.

Abstract

Gene Ontology consists of a controlled vocabulary of terms, annotating a gene or gene product, structured in a directed acyclic graph. In the graph, semantic relations connect the terms, that represent the knowledge of functional description and cellular component information of gene products. GO similarity gives us a numerical representation of biological relationship between a gene set, which can be used to infer various biological facts such as protein interaction, structural similarity, gene clustering, etc. Here we introduce a new shortest path based hybrid measure of ontological similarity between two terms which combines both structure of the GO graph and information content of the terms. Here the similarity between two terms t1 and t2, referred to as GOSimPBHM(t1; t2), has two components; one obtained from the common ancestors of t1 and t2. The other from their remaining ancestors. The proposed path based hybrid measure does not suffer from the well-known shallow annotation problem. Its superiority with respect to some other popular measure are proven through the various experiments.

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