Functional analysis tools for post-translational modification: a post-translational modification database for analysis of proteins and metabolic pathways
Functional analysis tools for post-translational modification: a post-translational modification database for analysis of proteins and metabolic pathways
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DOI：
10.1111/tpj.14372
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发表时间：
2019-09-01
期刊：
影响因子：
7.2
通讯作者：
Wallace, Ian S.
中科院分区：
文献类型：
--
作者：
Cruz, Edward R.;Nguyen, Hung;Wallace, Ian S.
翻译后修饰(PTM)是蛋白质功能的重要调节因子，目前已发现近200种不同类型的PTM。高分辨率质谱学的进展导致在许多生物体中发现了前所未有的PTM位点，潜在地促进了对PTM如何调控细胞行为的更全面的了解。虽然建立数据库是为了存放所产生的数据，但这些资源大多侧重于个别类型的技术转让，不考虑对技术转让进行量化分析，也不提供技术转让数据的可视化和分析工具。在这里，我们描述了翻译后修饰的功能分析工具(FAT-PTM)数据库()，它目前支持八种不同类型的PTM和超过49000个PTM位点，这些位点是在对模式生物拟南芥的大规模蛋白质组调查中确定的。FAT-PTM数据库目前支持可视化工具，以可视化以蛋白质为中心的PTM网络、来自10多个不同定量磷酸蛋白质组研究的定量磷酸化位点数据、以蛋白质为中心的代谢途径中显示的PTM信息以及由多个PTM共同修饰的蛋白质组。总体而言，FAT-PTM数据库为用户提供了一个强大的平台，以共享和可视化实验支持的PTM数据，开发与目标蛋白质相关的假说，或识别PTM数据中的信号和代谢途径的紧急模式。
Post-translational modifications (PTMs) are critical regulators of protein function, and nearly 200 different types of PTM have been identified. Advances in high-resolution mass spectrometry have led to the identification of an unprecedented number of PTM sites in numerous organisms, potentially facilitating a more complete understanding of how PTMs regulate cellular behavior. While databases have been created to house the resulting data, most of these resources focus on individual types of PTM, do not consider quantitative PTM analyses or do not provide tools for the visualization and analysis of PTM data. Here, we describe the Functional Analysis Tools for Post-Translational Modifications (FAT-PTM) database (), which currently supports eight different types of PTM and over 49 000 PTM sites identified in large-scale proteomic surveys of the model organism Arabidopsis thaliana. The FAT-PTM database currently supports tools to visualize protein-centric PTM networks, quantitative phosphorylation site data from over 10 different quantitative phosphoproteomic studies, PTM information displayed in protein-centric metabolic pathways and groups of proteins that are co-modified by multiple PTMs. Overall, the FAT-PTM database provides users with a robust platform to share and visualize experimentally supported PTM data, develop hypotheses related to target proteins or identify emergent patterns in PTM data for signaling and metabolic pathways.