INFORMATION CHANGE THE WORLD

International Journal of Information Technology and Computer Science(IJITCS)

ISSN: 2074-9007 (Print), ISSN: 2074-9015 (Online)

Published By: MECS Press

IJITCS Vol.3, No.2, Mar. 2011

On Construction of Gene-PDB Structure Mapping with Applications in Functional Annotation of Human Genes

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Author(s)

Xi Chen,Hao Jiang,Wai-Ki Ching,Limin Li

Index Terms

Classifiction, Gene Functions, Protein Structures, Prediction, Similarity

Abstract

Protein 3D structure is one of the key factors in recognizing gene functions. The availability of protein structure data in Protein Data Bank (PDB) enables us to conduct gene function analysis. However, the molecules in the PDB, whose structures have been determined, are always not corresponding to a unique gene. That is to say, the mapping from gene to PDB is not one-to-one. Thus this uncertain property complicates the analysis and increases the difficulty of gene function analysis. In this paper, we attempt to tackle this challenging issue and we study the problem of predicting gene function from protein structures based on the gene-PDB mapping. We first obtain the gene-PDB mapping, which is important in representing a gene by the structure set of all its corresponding PDB molecules. We then define a new gene-gene similarity measurement based on the structure similarity between PDB molecules. We further show that this new measurement matches with gene functional similarity nicely. This means that the measurement we introduced here can be useful for gene function prediction. Numerical examples are given to demonstrate our claim.

Cite This Paper

Xi Chen, Hao Jiang, Wai-Ki Ching, Limin Li, "On Construction of Gene-PDB Structure Mapping with Applications in Functional Annotation of Human Genes", International Journal of Information Technology and Computer Science(IJITCS), vol.3, no.2, pp.53-59, 2011. DOI: 10.5815/ijitcs.2011.02.08

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