PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database

@article{citeulike:3106721, abstract = {Motivation: To fully understand how a protein kinase regulates biological processes, it is imperative to first identify its substrate(s) and interacting protein(s). However, of the 518 known human serine/threonine/tyrosine kinases, 35\% of these have known substrates, while 14\% of the kinases have identified substrate recognition motifs. In contrast, 85\% of the kinases have protein-protein interaction (PPI) datasets, raising the possibility that we might reveal potential kinase-substrate pairs from these PPIs. Results: PhosphoPOINT, a comprehensive human kinase interactome and phospho-protein database, is a collection of 4195 phospho-proteins with a total of 15 738 phosphorylation sites. PhosphoPOINT annotates the interactions among kinases, with their down-stream substrates and with interacting (phospho)-proteins to modulate the kinase-substrate pairs. PhosphoPOINT implements various gene expression profiles and Gene Ontology cellular component information to evaluate each kinase and their interacting (phospho)-proteins/substrates. Integration of cSNPs that cause amino acids change with the proteins with the phosphoprotein dataset reveals that 64 phosphorylation sites result in a disease phenotypes when changed; the linked phenotypes include schizophrenia and hypertension. PhosphoPOINT also provides a search function for all phospho-peptides using about 300 known kinase/phosphatase substrate/binding motifs. Altogether, PhosphoPOINT provides robust annotation for kinases, their downstream substrates and their interaction (phospho)-proteins and this should accelerate the functional characterization of kinomemediated signaling. Availability: PhosphoPOINT can be freely accessed in http://kinase.bioinformatics.tw/ Contact: cyhuang5@ym.edu.tw; kmchao@csie.ntu.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btn297}, author = {Yang, Chia-Ying and Chang, Chao-Hui and Yu, Ya-Ling and Lin, Tsu-Chun E. and Lee, Sheng-An and Yen, Chueh-Chuan and Yang, Jinn-Moon and Lai, Jin-Mei and Hong, Yi-Ren and Tseng, Tzu-Ling and Chao, Kun-Mao and Huang, Chi-Ying F. }, citeulike-article-id = {3106721}, doi = {http://dx.doi.org/10.1093/bioinformatics/btn297}, journal = {Bioinformatics}, keywords = {bioinformatics, datamining, kinase, ressource}, month = {August}, number = {16}, pages = {i14--20}, posted-at = {2008-09-02 14:43:39}, priority = {0}, title = {PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database}, url = {http://dx.doi.org/10.1093/bioinformatics/btn297}, volume = {24}, year = {2008} }

TY - JOUR ID - citeulike:3106721 L3 - citeulike-article-id:3106721 N2 - Motivation: To fully understand how a protein kinase regulates biological processes, it is imperative to first identify its substrate(s) and interacting protein(s). However, of the 518 known human serine/threonine/tyrosine kinases, 35% of these have known substrates, while 14% of the kinases have identified substrate recognition motifs. In contrast, 85% of the kinases have protein-protein interaction (PPI) datasets, raising the possibility that we might reveal potential kinase-substrate pairs from these PPIs. Results: PhosphoPOINT, a comprehensive human kinase interactome and phospho-protein database, is a collection of 4195 phospho-proteins with a total of 15 738 phosphorylation sites. PhosphoPOINT annotates the interactions among kinases, with their down-stream substrates and with interacting (phospho)-proteins to modulate the kinase-substrate pairs. PhosphoPOINT implements various gene expression profiles and Gene Ontology cellular component information to evaluate each kinase and their interacting (phospho)-proteins/substrates. Integration of cSNPs that cause amino acids change with the proteins with the phosphoprotein dataset reveals that 64 phosphorylation sites result in a disease phenotypes when changed; the linked phenotypes include schizophrenia and hypertension. PhosphoPOINT also provides a search function for all phospho-peptides using about 300 known kinase/phosphatase substrate/binding motifs. Altogether, PhosphoPOINT provides robust annotation for kinases, their downstream substrates and their interaction (phospho)-proteins and this should accelerate the functional characterization of kinomemediated signaling. Availability: PhosphoPOINT can be freely accessed in http://kinase.bioinformatics.tw/ Contact: cyhuang5@ym.edu.tw; kmchao@csie.ntu.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btn297 IS - 16 JF - Bioinformatics EP - 20 TI - PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database VL - 24 SP - i14 KW - bioinformatics KW - datamining KW - kinase KW - ressource AU - Yang, Chia-Ying AU - Chang, Chao-Hui AU - Yu, Ya-Ling AU - Lin, Tsu-Chun AU - Lee, Sheng-An AU - Yen, Chueh-Chuan AU - Yang, Jinn-Moon AU - Lai, Jin-Mei AU - Hong, Yi-Ren AU - Tseng, Tzu-Ling AU - Chao, Kun-Mao AU - Huang, Chi-Ying PY - 2008/08/15/ UR - http://dx.doi.org/10.1093/bioinformatics/btn297 ER -