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Article: On construction of gene-PDB structure mapping with applications in functional annotation of human genes

TitleOn construction of gene-PDB structure mapping with applications in functional annotation of human genes
Authors
KeywordsClassifiction
Gene Functions
Protein Structures
Prediction
Similarity
Issue Date2011
PublisherModern Education & Computer Science Press. The Journal's web site is located at http://www.mecs-press.org/ijitcs/
Citation
International Journal of Information Technology and Computer Science, 2011, v. 3 n. 2, p. 53-59 How to Cite?
AbstractProtein 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.
Persistent Identifierhttp://hdl.handle.net/10722/135164
ISSN

 

DC FieldValueLanguage
dc.contributor.authorChen, Xen_US
dc.contributor.authorJiang, Hen_US
dc.contributor.authorChing, WKen_US
dc.contributor.authorLi, Len_US
dc.date.accessioned2011-07-27T01:29:11Z-
dc.date.available2011-07-27T01:29:11Z-
dc.date.issued2011en_US
dc.identifier.citationInternational Journal of Information Technology and Computer Science, 2011, v. 3 n. 2, p. 53-59en_US
dc.identifier.issn2074-9007-
dc.identifier.urihttp://hdl.handle.net/10722/135164-
dc.description.abstractProtein 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.-
dc.languageengen_US
dc.publisherModern Education & Computer Science Press. The Journal's web site is located at http://www.mecs-press.org/ijitcs/-
dc.relation.ispartofInternational Journal of Information Technology and Computer Scienceen_US
dc.rightsInternational Journal of Information Technology and Computer Science. Copyright © MECS Publisher-
dc.subjectClassifiction-
dc.subjectGene Functions-
dc.subjectProtein Structures-
dc.subjectPrediction-
dc.subjectSimilarity-
dc.titleOn construction of gene-PDB structure mapping with applications in functional annotation of human genesen_US
dc.typeArticleen_US
dc.identifier.emailChen, X: dlkcissy@hku.hken_US
dc.identifier.emailJiang, H: haohao@hkusuc.hku.hk-
dc.identifier.emailChing, WK: wching@hku.hk-
dc.identifier.authorityChing, WK=rp00679en_US
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.5815/ijitcs.2011.02.08-
dc.identifier.hkuros188184en_US
dc.identifier.volume3en_US
dc.identifier.issue2-
dc.identifier.spage53en_US
dc.identifier.epage59en_US
dc.publisher.placeHong Kong-

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