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Bioinformatics 2008 24(16):i14-i20; doi:10.1093/bioinformatics/btn297
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Chia-Ying Yang 1, Chao-Hui Chang 10, Ya-Ling Yu 4, Tsu-Chun Emma Lin 10, Sheng-An Lee 1, Chueh-Chuan Yen 5, Jinn-Moon Yang 6, Jin-Mei Lai 7, Yi-Ren Hong 8, Tzu-Ling Tseng 9, Kun-Mao Chao 1,2,3,* and Chi-Ying F. Huang 1,10,11,12,*

1Department of Computer Science and Information Engineering, 2Graduate Institute of Biomedical Electronics and Bioinformatics, 3Graduate Institute of Networking and Multimedia, National Taiwan University, Taipei 106, 4Graduate Institute of Life Sciences, National Defense Medical Center University, Taipei 114, 5Division of Hematology and Oncology, Department of Medicine, Taipei Veterans General Hospital, Taipei, 6Institute of Bioinformatics, National Chiao-Tung University, Hsinchu 300, 7Department of Life Science, Fu-Jen Catholic University, Taipei Hsinchuang 242, 8Department of Biochemistry, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, 9Department of Proteomics Technology, Industrial Technology Research Institute, 195, Section 4 Chung Hsing Road, Chutung, Hsinchu 310, 10Institute of Clinical Medicine, 11Institute of Bio-Pharmaceutical Sciences and 12Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan, Republic of China

*To whom correspondence should be addressed.


  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{at}ym.edu.tw; kmchao{at}csie.ntu.edu.tw

Supplementary information: Supplementary data are available at Bioinformatics online.


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