CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data.
CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data.
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DOI：
10.1091/mbc.e21-05-0257
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发表时间：
2021-11-01
影响因子：
3.3
通讯作者：
Torres JZ
中科院分区：
文献类型：
--
作者：
Velasquez EF;Garcia YA;Ramirez I;Gholkar AA;Torres JZ
阐明蛋白质的相互作用/缔合网络对于定义其生物学功能非常重要。基于质谱的蛋白质组学方法已成为识别蛋白质-蛋白质相互作用（PPIs）和蛋白质-蛋白质关联（PPA）的强大工具。然而，考虑到生成的数据的复杂性和丰富性，相互作用组/关联实验很难解释。尽管已经开发出定量识别蛋白质相互作用/关联的工具，但仍然迫切需要易于使用的工具，使用户能够将其结果结合起来。为了解决这个问题，我们开发了 CANVS，这是一种计算管道，可以清理、分析和可视化基于质谱的相互作用组/关联数据。 CANVS 被包装为一个具有简单要求的交互式 Shiny 仪表板，允许用户轻松与管道交互、分析复杂的实验数据并创建 PPI/A 网络。该应用程序集成了 BioGRID 和 CORUM 等系统生物学数据库，以将结果情境化。此外，CANVS 还具有基因本体论工具，允许用户识别结果中的相关 GO 术语，并使用与相关 GO 术语相关的蛋白质创建视觉网络。总体而言，CANVS 是一个易于使用的应用程序，使所有研究人员受益，特别是那些缺乏已建立的生物信息学流程并对研究相互作用组/关联数据感兴趣的人。
The elucidation of a protein’s interaction/association network is important for defining its biological function. Mass spectrometry–based proteomic approaches have emerged as powerful tools for identifying protein–protein interactions (PPIs) and protein–protein associations (PPAs). However, interactome/association experiments are difficult to interpret, considering the complexity and abundance of data that are generated. Although tools have been developed to identify protein interactions/associations quantitatively, there is still a pressing need for easy-to-use tools that allow users to contextualize their results. To address this, we developed CANVS, a computational pipeline that cleans, analyzes, and visualizes mass spectrometry–based interactome/association data. CANVS is wrapped as an interactive Shiny dashboard with simple requirements, allowing users to interface easily with the pipeline, analyze complex experimental data, and create PPI/A networks. The application integrates systems biology databases such as BioGRID and CORUM to contextualize the results. Furthermore, CANVS features a Gene Ontology tool that allows users to identify relevant GO terms in their results and create visual networks with proteins associated with relevant GO terms. Overall, CANVS is an easy-to-use application that benefits all researchers, especially those who lack an established bioinformatic pipeline and are interested in studying interactome/association data.
影响因子：
3.4
作者：
Nesvizhskii, Alexey I.
通讯作者：
Nesvizhskii, Alexey I.