Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.
Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.
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DOI：
10.1007/978-1-4939-6783-4_10
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发表时间：
2017
期刊：
影响因子：
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通讯作者：
Arighi CN
中科院分区：
文献类型：
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作者：
Wang Q;Ross KE;Huang H;Ren J;Li G;Vijay-Shanker K;Wu CH;Arighi CN
翻译后修饰（PTM）是蛋白质组学领域蛋白质组多样性的主要贡献者之一。特别是，蛋白质磷酸化代表了在许多生物过程中发挥作用的重要调节机制。蛋白激酶（催化这种反应的酶）是代谢和信号传导途径的关键参与者。它们的激活或失活决定下游事件：哪些底物被修饰及其随后的影响（例如激活状态、定位、蛋白质-蛋白质相互作用（PPI））。生物医学文献仍然是蛋白质磷酸化实验信息的主要证据来源。将磷酸化事件和磷酸化依赖性 PPI 结合在一起的自动方法有助于总结当前知识并揭示隐藏的联系。在本章中，我们演示了两种文本挖掘工具，RLIMS-P 和 eFIP，用于从文献中检索和提取激酶底物位点数据和磷酸化依赖性 PPI。与 PubMed 中的文献检索相比，这些工具具有多个优势，因为它们的结果针对磷酸化。 RLIMS-P 和 eFIP 结果可以通过多种方式进行排序、组织和查看，以回答相关的生物学问题，并且提及的蛋白质与 UniProt 标识符相关联。
Post-translational modifications (PTMs) are one of the main contributors to the diversity of proteoforms in the proteomic landscape. In particular, protein phosphorylation represents an essential regulatory mechanism that plays a role in many biological processes. Protein kinases, the enzymes catalyzing this reaction, are key participants in metabolic and signaling pathways. Their activation or inactivation dictate downstream events: what substrates are modified and their subsequent impact (e.g., activation state, localization, protein-protein interactions (PPIs)). The biomedical literature continues to be the main source of evidence for experimental information about protein phosphorylation. Automatic methods to bring together phosphorylation events and phosphorylation-dependent PPIs can help to summarize the current knowledge and to expose hidden connections. In this chapter, we demonstrate two text mining tools, RLIMS-P and eFIP, for the retrieval and extraction of kinase-substrate-site data and phosphorylation-dependent PPIs from the literature. These tools offer several advantages over a literature search in PubMed as their results are specific for phosphorylation. RLIMS-P and eFIP results can be sorted, organized, and viewed in multiple ways to answer relevant biological questions, and the protein mentions are linked to UniProt identifiers.