ABI Development: Integrative Bioinformatics for Knowledge Discovery of PTM Networks

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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).