RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.
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DOI：
10.1093/database/bau034
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Chen YJ
中科院分区：
文献类型：
--
作者：
Huang KY;Wu HY;Chen YJ;Lu CT;Su MG;Hsieh YC;Tsai CM;Lin KI;Huang HD;Lee TY;Chen YJ
激酶催化的蛋白质磷酸化在调节多种细胞内过程中起着至关重要的作用。由于基于质谱 (MS) 的蛋白质组学已鉴定出越来越多的体内磷酸化位点，因此开发了 RegPhos（可在线获取 http://csb.cse.yzu.edu.tw/RegPhos2/）来探索人类中的蛋白质磷酸化网络。在本次更新中，我们不仅增强了人类的数据内容，还研究了小鼠和大鼠的激酶底物磷酸化网络。经过实验验证的磷酸化位点及其催化激酶是从公共资源中提取的，MS/MS 磷酸肽是从研究文章中手动策划的。 RegPhos 2.0旨在通过整合代谢途径和蛋白质-蛋白质相互作用的信息，提供更全面的细胞内信号网络视图。案例研究表明，通过分析液相色谱-质谱 (LC-MS/MS) 分析获得的时间依赖性细胞激活的磷酸化蛋白质组谱，RegPhos 不仅破译了 B 细胞受体 (BCR) 信号通路中的一致方案，还破译了可能参与其中的新型调节分子。为了帮助用户有效地识别癌症中的候选生物标志物，我们对 30 个微阵列实验（包括 39 个癌细胞与正常细胞）进行了分析，以检测编码激酶及其底物的癌症特异性表达基因。此外，此更新还改进了网络界面，以便于方便地访问一组基因/蛋白质的磷酸化网络。数据库网址：http://csb.cse.yzu.edu.tw/RegPhos2/
Protein phosphorylation catalyzed by kinases plays crucial roles in regulating a variety of intracellular processes. Owing to an increasing number of in vivo phosphorylation sites that have been identified by mass spectrometry (MS)-based proteomics, the RegPhos, available online at http://csb.cse.yzu.edu.tw/RegPhos2/, was developed to explore protein phosphorylation networks in human. In this update, we not only enhance the data content in human but also investigate kinase–substrate phosphorylation networks in mouse and rat. The experimentally validated phosphorylation sites as well as their catalytic kinases were extracted from public resources, and MS/MS phosphopeptides were manually curated from research articles. RegPhos 2.0 aims to provide a more comprehensive view of intracellular signaling networks by integrating the information of metabolic pathways and protein–protein interactions. A case study shows that analyzing the phosphoproteome profile of time-dependent cell activation obtained from Liquid chromatography-mass spectrometry (LC-MS/MS) analysis, the RegPhos deciphered not only the consistent scheme in B cell receptor (BCR) signaling pathway but also novel regulatory molecules that may involve in it. With an attempt to help users efficiently identify the candidate biomarkers in cancers, 30 microarray experiments, including 39 cancerous versus normal cells, were analyzed for detecting cancer-specific expressed genes coding for kinases and their substrates. Furthermore, this update features an improved web interface to facilitate convenient access to the exploration of phosphorylation networks for a group of genes/proteins. Database URL: http://csb.cse.yzu.edu.tw/RegPhos2/
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影响因子：
3
作者：
Huang, HD;Lee, TY;Huang, KT
通讯作者：
Huang, KT
影响因子：
5.5
作者：
Cheung, Ricky;Malik, Mobeen;Collman, Ronald G.
通讯作者：
Collman, Ronald G.
影响因子：
3
作者：
Durek P;Schudoma C;Weckwerth W;Selbig J;Walther D
通讯作者：
Walther D
影响因子：
14.9
作者：
Hornbeck PV;Kornhauser JM;Tkachev S;Zhang B;Skrzypek E;Murray B;Latham V;Sullivan M
通讯作者：
Sullivan M
PathFinder：从蛋白质-蛋白质相互作用网络中挖掘信号转导途径片段。
影响因子：
3
作者：
Bebek, Gurkan;Yang, Jiong
通讯作者：
Yang, Jiong