標題: RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans
作者: Lee, Tzong-Yi
Hsu, Justin Bo-Kai
Chang, Wen-Chi
Huang, Hsien-Da
生物科技學系
資訊工程學系
Department of Biological Science and Technology
Department of Computer Science
公開日期: 1-Jan-2011
摘要: Protein phosphorylation catalyzed by kinases plays crucial regulatory roles in intracellular signal transduction. With the increasing number of experimental phosphorylation sites that has been identified by mass spectrometry-based proteomics, the desire to explore the networks of protein kinases and substrates is motivated. Manning et al. have identified 518 human kinase genes, which provide a starting point for comprehensive analysis of protein phosphorylation networks. In this study, a knowledgebase is developed to integrate experimentally verified protein phosphorylation data and protein-protein interaction data for constructing the protein kinase-substrate phosphorylation networks in human. A total of 21 110 experimental verified phosphorylation sites within 5092 human proteins are collected. However, only 4138 phosphorylation sites (similar to 20%) have the annotation of catalytic kinases from public domain. In order to fully investigate how protein kinases regulate the intracellular processes, a published kinase-specific phosphorylation site prediction tool, named KinasePhos is incorporated for assigning the potential kinase. The web-based system, RegPhos, can let users input a group of human proteins; consequently, the phosphorylation network associated with the protein subcellular localization can be explored. Additionally, time-coursed microarray expression data is subsequently used to represent the degree of similarity in the expression profiles of network members. A case study demonstrates that the proposed scheme not only identify the correct network of insulin signaling but also detect a novel signaling pathway that may cross-talk with insulin signaling network. This effective system is now freely available at http://RegPhos.mbc.nctu.edu.tw.
URI: http://dx.doi.org/10.1093/nar/gkq970
http://hdl.handle.net/11536/26052
ISSN: 0305-1048
DOI: 10.1093/nar/gkq970
期刊: NUCLEIC ACIDS RESEARCH
Volume: 39
Issue: 
起始頁: D777
結束頁: D787
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