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论文题目: Construction and Deciphering of Human Phosphorylation-Mediated Signaling Transduction Networks
英文论文题目: Construction and Deciphering of Human Phosphorylation-Mediated Signaling Transduction Networks
第一作者: Zhang, MH; Li, H; He, Y; Sun, H; Xia, L; Wang, LS; Sun, B; Ma, LX; Zhang, GQ; Li, J; Li, YX; Xie, L
英文第一作者: Zhang, MH; Li, H; He, Y; Sun, H; Xia, L; Wang, LS; Sun, B; Ma, LX; Zhang, GQ; Li, J; Li, YX; Xie, L
联系作者: Li, J (reprint author), Shanghai Jiao Tong Univ, Dept Bioinformat & Biostat, Sch Life Sci & Biotechnol, Shanghai 200240, Peoples R China.
英文联系作者: Li, J (reprint author), Shanghai Jiao Tong Univ, Dept Bioinformat & Biostat, Sch Life Sci & Biotechnol, Shanghai 200240, Peoples R China.
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发表年度: 2015
卷: 14
期: 7
页码: 2745-2757
摘要: Protein phosphorylation is the most abundant reversible covalent modification. Human protein kinases participate in almost all biological pathways, and approximately half of the kinases are associated with disease. PhoSigNet was designed to store and display human phosphorylation-mediated signal transduction networks, with additional information related to cancer. It contains 11 976 experimentally validated directed edges and 216 871 phosphorylation sites. Moreover, 3491 differentially expressed proteins in human cancer from dbDEPC, 18 907 human cancer variation sites from CanProVar, and 388 hyperphosphorylation sites from PhosphoSitePlus were collected as annotation information. Compared with other phosphorylation-related databases, PhoSigNet not only takes the kinase-substrate regulatory relationship pairs into account, but also extends regulatory relationships up- and downstream (e.g., from ligand to receptor, from G protein to kinase, and from transcription factor to targets). Furthermore, PhoSigNet allows the user to investigate the impact of phosphorylation modifications on cancer. By using one set of in-house time series phosphoproteomics data, the reconstruction of a conditional and dynamic phosphorylation-mediated signaling network was exemplified. We expect PhoSigNet to be a useful database and analysis platform benefiting both proteomics and cancer studies.
英文摘要: Protein phosphorylation is the most abundant reversible covalent modification. Human protein kinases participate in almost all biological pathways, and approximately half of the kinases are associated with disease. PhoSigNet was designed to store and display human phosphorylation-mediated signal transduction networks, with additional information related to cancer. It contains 11 976 experimentally validated directed edges and 216 871 phosphorylation sites. Moreover, 3491 differentially expressed proteins in human cancer from dbDEPC, 18 907 human cancer variation sites from CanProVar, and 388 hyperphosphorylation sites from PhosphoSitePlus were collected as annotation information. Compared with other phosphorylation-related databases, PhoSigNet not only takes the kinase-substrate regulatory relationship pairs into account, but also extends regulatory relationships up- and downstream (e.g., from ligand to receptor, from G protein to kinase, and from transcription factor to targets). Furthermore, PhoSigNet allows the user to investigate the impact of phosphorylation modifications on cancer. By using one set of in-house time series phosphoproteomics data, the reconstruction of a conditional and dynamic phosphorylation-mediated signaling network was exemplified. We expect PhoSigNet to be a useful database and analysis platform benefiting both proteomics and cancer studies.
刊物名称: JOURNAL OF PROTEOME RESEARCH
英文刊物名称: JOURNAL OF PROTEOME RESEARCH
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学科: Biochemistry & Molecular Biology
英文学科: Biochemistry & Molecular Biology
影响因子: 4.245
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论文类别: Article
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