PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome.
Recent progress in identification and mapping of single nucleotide polymorphisms (SNPs) in the human genome generates an unprecedented opportunity to explore cause-effect relationships between genetic variations and susceptibility to common diseases. For this purpose, one promising strategy would be to select a set of SNPs that potentially alter the function of proteins involved in the pathogenesis of the diseases and compare their frequencies in the affected individuals and the healthy population. In this respect, SNPs that change amino acid sequences (nonsynonymous SNPs; nsSNPs) are of particular interest, since they are more likely to affect protein functions. In this study, we have constructed a catalog of nsSNPs (PicSNP), whose unique features are (i) nsSNPs are classified according to the functions of the affected genes and are searchable under the guidance of hierarchical lists of protein functions and (ii) nsSNPs that lead to amino acid changes in the known functional sites and domains of proteins are highlighted. Out of 1,190,295 SNPs extracted from public database, we identified 3793 nsSNPs and classified them in 1247 categories of protein functions. 495 sites and domains annotated in the Swiss-Prot database were found to include nsSNPs, including 2 nsSNPs in disulfide-binding sites and 38 nsSNPs in transmembrane regions. PicSNP is available via the World Wide Web (http://picsnp.org) and would support research questing for SNPs involved in common diseases.
Chang
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Health Service Center, Department of Internal Medicine, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan. hchang-tky@umin.ac.jp
Fujita
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D016208:Databases, Factual; D015894:Genome, Human; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017434:Protein Structure, Tertiary; D012984:Software