Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle

Aidan P. Tay; Angelita Liang; Marc R. Wilkins

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Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle

机译：使用PTMORACLE可视化蛋白质交互网络的翻译后修改

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Post-translational modifications (PTMs) of proteins act as key regulators of protein activity, including the regulation of protein-protein interactions (PPIs). However, exploring functional links between PTMs and PPIs can be difficult. PTMOracle is aCytoscape app that facilitates the co-visualization and co-analysis of PTMs in the context of PPI networks. PTMOracle also allows extensive data to be integrated and co-analyzed, allowing the role of domains, motifs, and disordered regions to be considered. Here, we describe several PTMOracle protocols investigating complex PTM-associated relationships and their role in PPIs. This is assisted by OraclePainter for coloring proteins by the modifications present and visualizing these in the context of networks, by OracleTools for cross-matching PTMs with sequence feature for all nodes in the network, and by OracleResults for exploring specific proteins and visualizing their PTMs in the context of protein sequences. This unit aims to demonstrate how PTMOracle can be used to systematically explore network visualizations and generate testable hypotheses regarding the functional role of PTMs in PPIs, and how the results can be analyzed to better understand the regulatory role of PTMs in PPIs.

机译：蛋白质的翻译后修饰（PTMS）作为蛋白质活性的关键调节剂，包括调节蛋白质 - 蛋白质相互作用（PPI）。然而，探索PTM和PPI之间的功能链接可能是困难的。 PTMORACLE是ACYTOSCAPE应用程序，促进PPI网络上下文中PTM的共识和共同分析。 PTMoracle还允许广泛的数据集成和共同分析，允许考虑域，图案和混乱区域的作用。在这里，我们描述了几种调查了复杂的PTM相关关系的PTMoracle协议及其在PPI中的角色。这是由OraclePainter辅助的，用于通过存在的修改和在网络的上下文中进行着色蛋白，通过oracletools与网络中所有节点的序列特征交叉匹配ptms，以及oracleresults探索特定蛋白质并在中断其ptms蛋白质序列的背景。本机旨在展示PTMoracle如何用于系统地探索网络可视化并产生关于PPI中PTM的功能作用的可测试假设，以及如何分析结果以更好地理解PPI中PTM的调节作用。

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来源
《Current Protocols in Bioinformatics》 |2019年第1期|共23页
作者
Aidan P. Tay; Angelita Liang; Marc R. Wilkins;
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作者单位

Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney New South Wales Australia;

Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney New South Wales Australia;

Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney New South Wales Australia;

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正文语种 eng
中图分类遗传学;
关键词
Cytoscape; data integration; network visualization; post-translational modification; protein-protein interaction;

机译：Cytoscape;数据集成;网络可视化;翻译后修饰;蛋白质 - 蛋白质相互作用;

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专利

1. Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle [J] . Aidan P. Tay, Angelita Liang, Marc R. Wilkins Current Protocols in Bioinformatics . 2019,第1期

机译：使用PTMORACLE可视化蛋白质交互网络的翻译后修改
2. The Roles of Post-translational Modifications in the Context of Protein Interaction Networks [J] . Guangyou Duan, Dirk Walther PLoS Computational Biology . 2015,第2期

机译：翻译后修饰在蛋白质相互作用网络中的作用
3. The Roles of Post-translational Modifications in the Context of Protein Interaction Networks [J] . Guangyou Duan, Dirk Walther PLoS Computational Biology . 2015,第2期

机译：翻译后修饰在蛋白质相互作用网络中的作用
4. Identification of Specific Protein-Protein Interactions via Detecting Post-Translational Modifications [C] . I-Hsuan (Blair) Chen, Meng-Chieh Chen, Xiao-qi Liu, ASMS Conference on Mass Spectrometry and Allied Topics . 2015

机译：通过检测翻译后修改鉴定特定的蛋白质 - 蛋白质相互作用
5. Biochemical Studies of the CTCF Insulator Protein: Determination of Protein Interactions with CTCF using Tandem Affinity Purification, Characterization of its Post-translational Modification by the Small Ubiquitin-like Modifier Proteins and Studies of CTCF DNA Looping Ability [D] . MacPherson, Melissa Jean 2010

机译：CTCF绝缘子蛋白的生化研究：使用串联亲和纯化确定蛋白与CTCF的相互作用，小泛素样修饰蛋白对其翻译后修饰的表征以及CTCF DNA环状能力的研究
6. The Roles of Post-translational Modifications in the Context of Protein Interaction Networks [O] . Guangyou Duan, Dirk Walther 2015

机译：翻译后修饰在蛋白质相互作用网络中的作用
7. The roles of post-translational modifications in the context of protein interaction networks. [O] . Guangyou Duan, Dirk Walther 2015

机译：翻译后修饰在蛋白质相互作用网络中的作用。

Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle

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