Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, USA.
Center for Bioinformatics & Computational Biology; University of Delaware, USA.
Nucleic Acids Res. 2020 Jul 2;48(W1):W85-W93. doi: 10.1093/nar/gkaa436.
Rapid progress in proteomics and large-scale profiling of biological systems at the protein level necessitates the continued development of efficient computational tools for the analysis and interpretation of proteomics data. Here, we present the piNET server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with the LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. The primary input for the server consists of a set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. Several interconnected workflows can be used to generate: (i) interactive graphs and tables providing comprehensive annotation and mapping between peptides and proteins with PTM sites; (ii) high resolution and interactive visualization for enzyme-substrate networks, including kinases and their phospho-peptide targets; (iii) mapping and visualization of LINCS signature connectivity for chemical inhibitors or genetic knockdown of enzymes upstream of their target PTM sites. piNET has been built using a modular Spring-Boot JAVA platform as a fast, versatile and easy to use tool. The Apache Lucene indexing is used for fast mapping of peptides into UniProt entries for the human, mouse and other commonly used model organism proteomes. PTM-centric network analyses combine PhosphoSitePlus, iPTMnet and SIGNOR databases of validated enzyme-substrate relationships, for kinase networks augmented by DeepPhos predictions and sequence-based mapping of PhosphoSitePlus consensus motifs. Concordant LINCS signatures are mapped using iLINCS. For each workflow, a RESTful API counterpart can be used to generate the results programmatically in the json format. The server is available at http://pinet-server.org, and it is free and open to all users without login requirement.
蛋白质组学的快速发展和在蛋白质水平上对生物系统的大规模分析使得开发高效的计算工具来分析和解释蛋白质组学数据成为必要。在这里，我们介绍了 piNET 服务器，它可以方便地对定量蛋白质组学数据进行集成注释、分析和可视化，重点是 PTM 网络以及与 LINCS 化学和遗传扰动特征库的整合，以便提供进一步的机制和功能见解。该服务器的主要输入是一组肽或蛋白质，可选地带有 PTM 位点及其相应的丰度值。可以使用几个相互关联的工作流程来生成：（i）交互式图形和表格，提供带有 PTM 位点的肽和蛋白质之间的全面注释和映射；（ii）酶-底物网络的高分辨率和交互式可视化，包括激酶及其磷酸肽靶标；（iii）化学抑制剂或其靶标 PTM 位点上游酶的遗传敲低的 LINCS 特征连接性的映射和可视化。piNET 是使用模块化的 Spring-Boot JAVA 平台构建的，是一种快速、通用且易于使用的工具。Apache Lucene 索引用于快速将肽映射到 UniProt 条目，适用于人类、小鼠和其他常用模型生物的蛋白质组。以 PTM 为中心的网络分析结合了 PhosphoSitePlus、iPTMnet 和 SIGNOR 数据库中经过验证的酶-底物关系，用于激酶网络，增加了 DeepPhos 预测和 PhosphoSitePlus 共识基序的基于序列的映射。使用 iLINCS 映射一致的 LINCS 特征。对于每个工作流程，都可以使用 RESTful API 来以 json 格式以编程方式生成结果。该服务器可在 http://pinet-server.org 上获得，无需登录即可免费向所有用户开放。
