Detection and analysis of disease-associated single nucleotide polymorphism influencing post-translational modification

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Post-translational modification (PTM) plays a crucial role in biological functions and corresponding disease developments. Discovering disease-associated non-synonymous SNPs (nsSNPs) altering PTM sites can help to estimate the various PTM candidates involved in diseases, therefore, an integrated analysis between SNPs, PTMs and diseases is necessary. However, only a few types of PTMs affected by nsSNPs have been studied without considering disease-association until now. In this study, we developed a new database called PTM-SNP which contains a comprehensive collection of human nsSNPs that affect PTM sites, together with disease information. Total 179,325 PTM-SNPs were collected by aligning missense SNPs and stop-gain SNPs on PTM sites (position 0) or their flanking region (position -7 to 7). Disease-associated SNPs from GWAS catalogs were also matched with detected PTM-SNP to find disease associated PTM-SNPs. Our result shows PTM-SNPs are highly associated with diseases, compared with other nsSNP sites and functional classes including near gene, intron and so on. PTM-SNP can provide an insight about discovering important PTMs involved in the diseases easily through the web site. PTM-SNP is freely available at http://gcode.kaist.ac.kr/ptmsnp.
Publisher
BIOMED CENTRAL LTD
Issue Date
2015
Language
English
Article Type
Article
Keywords

GENOME-WIDE ASSOCIATION; PHOSPHORYLATION SITES; DATABASE; TOOL; CANCER; LOCI; SNPS

Citation

BMC MEDICAL GENOMICS, v.8

ISSN
1755-8794
DOI
10.1186/1755-8794-8-S2-S7
URI
http://hdl.handle.net/10203/211888
Appears in Collection
BiS-Journal Papers(저널논문)
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