TY - JOUR
T1 - DbSAP
T2 - Single amino-acid polymorphism database for protein variation detection
AU - Cao, Ruifang
AU - Shi, Yan
AU - Chen, Shuangguan
AU - Ma, Yimin
AU - Chen, Jiajun
AU - Yang, Juan
AU - Chen, Geng
AU - Shi, Tieliu
N1 - Publisher Copyright:
© 2016 The Author(s).
PY - 2017/1/1
Y1 - 2017/1/1
N2 - Millions of human single nucleotide polymorphisms (SNPs) or mutations have been identified so far, and these variants could be strongly correlated with phenotypic variations of traits/diseases. Among these variants, non-synonymous ones can result in aminoacid changes that are called single amino-acid polymorphisms (SAPs). Although some studies have tried to investigate the SAPs, only a small fraction of SAPs have been identified due to inadequately inferred protein variation database and the low coverage of mass spectrometry (MS) experiments. Here, we present the dbSAP database for conveniently accessing the comprehensive information and relationships of spectra, peptides and proteins of SAPs, as well as related genes, pathways, diseases and drug targets. In order to fully explore human SAPs, we built a customized protein database that contained comprehensive variant proteins by integrating and annotating the human SNPs and mutations from eight distinct databases (UniProt, Protein Mutation Database, HPMD, MSIPI, MS-CanProVar, dbSNP, Ensembl and COSMIC). After a series of quality controls, a total of 16 854 SAP peptides involving in 439 537 spectra were identified with large scale MS datasets from various human tissues and cell lines. dbSAP is freely available at http://www.megabionet. org/dbSAP/index.html.
AB - Millions of human single nucleotide polymorphisms (SNPs) or mutations have been identified so far, and these variants could be strongly correlated with phenotypic variations of traits/diseases. Among these variants, non-synonymous ones can result in aminoacid changes that are called single amino-acid polymorphisms (SAPs). Although some studies have tried to investigate the SAPs, only a small fraction of SAPs have been identified due to inadequately inferred protein variation database and the low coverage of mass spectrometry (MS) experiments. Here, we present the dbSAP database for conveniently accessing the comprehensive information and relationships of spectra, peptides and proteins of SAPs, as well as related genes, pathways, diseases and drug targets. In order to fully explore human SAPs, we built a customized protein database that contained comprehensive variant proteins by integrating and annotating the human SNPs and mutations from eight distinct databases (UniProt, Protein Mutation Database, HPMD, MSIPI, MS-CanProVar, dbSNP, Ensembl and COSMIC). After a series of quality controls, a total of 16 854 SAP peptides involving in 439 537 spectra were identified with large scale MS datasets from various human tissues and cell lines. dbSAP is freely available at http://www.megabionet. org/dbSAP/index.html.
UR - https://www.scopus.com/pages/publications/85016160793
U2 - 10.1093/nar/gkw1096
DO - 10.1093/nar/gkw1096
M3 - 文章
C2 - 27903894
AN - SCOPUS:85016160793
SN - 0305-1048
VL - 45
SP - D827-D832
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -
