ABI Development: Integrative Bioinformatics for Knowledge Discovery of PTM Networks

特拉华大学获得一笔赠款，用于开发生物信息学研究基础设施，用于在系统生物学背景下对植物蛋白质翻译后修饰(PTM)进行综合理解。虽然PTMS通过调节蛋白质的功能、活性和细胞定位在许多生物学过程中发挥着关键作用，但目前研究PTMS的研究框架仍然存在严重的空白。为了支持植物中重要的PTM的研究--磷酸化、糖基化、乙酰化、肉豆蔻化和泛素化--该项目将文本挖掘、数据挖掘、数据分析和可视化工具以及数据库和本体论整合到一个交叉研究资源中，以解决在探索和发现PTM网络方面的知识差距。开发了植物特有资源iPTMnet，以获取相关的PTM信息及其功能影响，如相互作用蛋白、功能、途径、亚细胞位置、表达和相关表型。基本的生物信息学框架连接PTM酶-底物关系，连接可能协同工作的主要PTM，并将PTM形式与生物上下文和跨分类群连接起来。该门户网站将零散的零星信息统一到具有生物学意义的上下文中，允许生物学家在蛋白质网络和路径图中搜索、浏览和可视化PTM，执行用例，并通过社区注释获取专家知识。开发了科学案例研究，以展示用于假设生成的综合生物信息学方法，以及在电子分析中选定的实验室验证。IPTMnet生物信息学资源采用共同标准，以促进广泛传播的互操作性。植物PTM生物信息学研讨会在植物蛋白磷酸化研讨会上举办，以吸引植物研究人员作为用户和合作者，促进社区注释和基础设施发展。外联工作包括作为在线资源的教程、用例和培训材料，以及在会议和大学举办的培训讲习班，特别是EPSCoR机构。该研究项目被纳入本科和研究生课程以及地区机构学生的研究实习，这些机构包括高中、本科生和少数民族机构。这一生物信息学网络基础设施填补了在理解PTM网络方面的知识空白，并将促进对PTM介导的生物过程的基本理解和植物生物学中新知识的发现。这个ABI开发项目产生的资源和研究成果与蛋白质信息资源(PIR)的生物信息学基础设施相结合，并可由广泛的研究社区在Web(http://proteininformationresource.org/iPTMnet).上访问

The University of Delaware is awarded a grant to develop a bioinformatics research infrastructure for integrated understanding of plant protein post-translational modifications (PTMs) in a systems biology context. While PTMs play a pivotal role in numerous biological processes by modulating regulation of protein function, activity and cellular localization, critical gaps remain in the current research framework for studying PTMs. To support the studies of important PTMs in plants -- phosphorylation, glycosylation, acetylation, myristoylation and ubiquitination -- this project integrates text mining, data mining, data analysis and visualization tools, and databases and ontologies into a cross-cutting research resource needed to address the knowledge gaps in exploring and discovering PTM networks. A plant-specific resource, iPTMnet, is developed to capture relevant PTM information and their functional impact, such as interacting proteins, function, pathway, subcellular location, expression, and associated phenotypes. The underlying bioinformatics framework connects PTM enzyme-substrate relationships, connects major PTMs that may work in concert, and connects PTM forms to biological contexts and across taxa. The web portal unifies the fragmented and sporadic information into a biologically meaningful context, allowing biologists to search, browse, visualize PTM in protein networks and pathway maps, conduct use cases, and capture expert knowledge via community annotation. Scientific case studies are developed to demonstrate the integrative bioinformatics approach for hypothesis generation, coupled with lab validation of selected in silico analysis. The iPTMnet bioinformatics resource adopts common standards to promote interoperability for broad dissemination. The Plant PTM Bioinformatics workshops are hosted at the Symposium on Plant Protein Phosphorylation to engage plant researchers as users and collaborators to advance community annotation and infrastructure development. Outreach effort includes tutorials, use cases and training materials as on-line resources, and training workshops at conferences and universities, especially EPSCoR institutions. This research project is incorporated into undergraduate and graduate course curriculum as well as research internships for students from area institutions, including high schools, undergraduate and minority institutions. This bioinformatics cyberinfrastructure addresses the knowledge gaps in the understanding of PTM networks and will facilitate the basic understanding of PTM-mediated biological processes and discovery of new knowledge in plant biology. The resource and research outcomes produced by this ABI Development project are integrated with the bioinformatics infrastructure at the Protein Information Resource (PIR) and accessible by the broad research community on the web (http://proteininformationresource.org/iPTMnet).