motifeR: An Integrated Web Software for Identification and Visualization of Protein Post‐Translational Modification Motifs
motifeR: An Integrated Web Software for Identification and Visualization of Protein Post‐Translational Modification Motifs
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omoteR：用于识别和可视化蛋白质翻译后修饰基序的集成网络软件
DOI：
10.1002/pmic.201900245
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发表时间：
2019
期刊：
影响因子：
3.4
通讯作者：
Hao Yang
中科院分区：
文献类型：
--
作者：
Shisheng Wang;Yue Cai;Jingqiu Cheng;Wenxue Li;Yansheng Liu;Hao Yang
随着通过质谱鉴定蛋白质翻译后修饰的应用的指数增长，发现和呈现这些修饰位点周围的基序变得越来越理想。尽管正在设计一些工具，但仍然缺乏有效和多功能的软件进行此类分析和说明。在这项研究中，开发了一个通用的和用户友好的网络工具，motifeR，用于从大型数据集中提取和可视化统计上显着的图案。特别是，还集成了多个功能，用于处理多修饰位点富集。公共数据集应用于测试其可用性，表明一些并发的修饰位点可能形成基序，并且具有低位置概率的肽可能不会被随机识别，并且可以被包括以支持基序发现。此外，对于人类磷酸化蛋白质组学数据集，可以通过基于NetworkKIN数据库组合激酶-底物关系来估计和建模差异激酶信号网络的表征，作为用户的可选功能。motifeR工具包可以方便地由任何科学团体或个人操作，即使是那些没有任何生物信息学背景的人，也可以在https://www.omicsolution.org/wukong/motifeR上免费获得。
With an exponential growth in applications identifying protein post‐translational modifications via mass spectrometry, discovery and presentation of motifs surrounding those modification sites have become increasingly desirable. Despite a few tools being designed, there is still a scarcity of effective and polyfunctional software for such analysis and illustrations. In this study, a versatile and user‐friendly web tool is developed, motifeR, for extracting and visualizing statistically significant motifs from large datasets. Particularly, several functions are also integrated for processing multi‐modification sites enrichment. Public datasets are applied to test their usability, indicating that some concurrent modification sites may form motifs and that peptides with low location probability may be not identified randomly and can be included to support motif discovery. In addition, for human phosphoproteomics datasets, the characterization of differential kinase signaling networks can be estimated and modeled by combining kinase‐substrate relations based on the NetworKIN database as an optional feature for users. The motifeR toolkit can be conveniently operated by any scientific community or individuals, even those without any bioinformatics background and is freely available at https://www.omicsolution.org/wukong/motifeR.