PhosphoPOINT: A comprehensive human kinase interactome and phospho-protein database
Journal
Bioinformatics
Journal Volume
24
Journal Issue
16
Pages
i14-i20
Date Issued
2008
Author(s)
Yang, C.-Y. et al.
Chang, C.-H.
Yu, Y.-L.
Lin, T.-C.E.
Lee, S.-A.
Yen, C.-C.
Yang, J.-M.
Lai, J.-M.
Hong, Y.-R.
Tseng, T.-L.
Huang, Chi-Ying F.
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. ? The Author 2008. Published by Oxford University Press. All rights reserved.
SDGs
Other Subjects
ATM protein; aurora A kinase; cyclin dependent kinase 5; G protein coupled receptor kinase; mitogen activated protein kinase 1; mitogen activated protein kinase 3; phosphoprotein; phosphotransferase; protein p53; rhodopsin kinase; amino acid substitution; computer program; conference paper; controlled study; enzyme substrate complex; gene expression profiling; human; hypertension; phenotypic variation; priority journal; protein database; protein motif; protein phosphorylation; protein protein interaction; schizophrenia; signal transduction; single nucleotide polymorphism; Binding Sites; Databases, Protein; Humans; Information Storage and Retrieval; Phosphoproteins; Phosphorylation; Phosphotransferases; Protein Binding; Protein Interaction Mapping; Proteome; User-Computer Interface
Type
conference paper