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


BACKGROUND
PhosphoPOINT can be freely accessed in http://kinase. bioinformatics.tw/.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Yang
Chia-Ying
CY
Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan, Republic of China.
Chang
Chao-Hui
CH
Yu
Ya-Ling
YL
Lin
Tsu-Chun Emma
TC
Lee
Sheng-An
SA
Yen
Chueh-Chuan
CC
Yang
Jinn-Moon
JM
Lai
Jin-Mei
JM
Hong
Yi-Ren
YR
Tseng
Tzu-Ling
TL
Chao
Kun-Mao
KM
Huang
Chi-Ying F
CY
D001665:Binding Sites; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D010750:Phosphoproteins / Q000737:chemistry / Q000378:metabolism*; D010766:Phosphorylation; D010770:Phosphotransferases / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D014584:User-Computer Interface
D010750:Phosphoproteins; D020543:Proteome; D010770:Phosphotransferases