Inferring Functional Annotation for Human Genes from Gene-PDB Structure Mapping

Abstract:

Protein 3D structure is one of the main factors in reecting gene functions. The availability of protein structure data in Protein Data Bank (PDB) allows us to conduct gene function analysis based on protein structure data. However, the molecules in PDB, whose structures having been determined, are always not corresponding to a unique gene. That is to say, the mapping from a gene to the PDB is not one-to-one. This feature complicates the situation and increases the difculty of gene function analysis. In this paper, we attempt to tackle this problem and also study the problem of predicting gene function from protein structures based on the gene-PDB mapping. We rst obtain the gene-PDB mapping, which is used to represent a gene by the structure set of all its corresponding PDB molecules. We then dene a new gene-gene similarity measurement based on the structure similarity between PDB molecules, and we further show that this new measurement matches with the gene functional similarity. This means that the measurement we dened here can be used effectively for gene function prediction.

• Periodical: Applied Mechanics and Materials (Volumes 195-196)
• Pages: 391-396
• DOI: https://doi.org/10.4028/www.scientific.net/AMM.195-196.391
• Online since: August 2012
• Authors: Xi Chen, Hao Jiang, Wai Ki Ching, Li Min Li
• Keywords: Classiction, Gene Functions, Prediction, Protein Structures, Similarity

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