Abstract
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach—combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species. iPTMnet encompasses data from (i) our PTM-focused text mining tools, RLIMS-P and eFIP, which extract phosphorylation information from full-scale mining of PubMed abstracts and full-length articles; (ii) a set of curated databases with experimentally observed PTMs; and iii) Protein Ontology that organizes proteins and PTM proteoforms, enabling their representation, annotation and comparison within and across species. Presently covering eight major PTM types (phosphorylation, ubiquitination, acetylation, methylation, glycosylation, S-nitrosylation, sumoylation and myristoylation), iPTMnet knowledgebase contains more than 654 500 unique PTM sites in over 62 100 proteins, along with more than 1200 PTM enzymes and over 24 300 PTM enzyme-substrate-site relations. The website supports online search, browsing, retrieval and visual analysis for scientific queries. Several examples, including functional interpretation of phosphoproteomic data, demonstrate iPTMnet as a gateway for visual exploration and systematic analysis of PTM networks and conservation, thereby enabling PTM discovery and hypothesis generation.
Highlights
Proteins are the link between biological information in the genome and the function of cells and organisms
We have established an automated workflow for full-scale processing of all PubMed abstracts and full length articles of the PubMed Central Open Access set (PMCOA) with RLIMS-P and eFIP, which have been previously evaluated for performance and usability in community challenges [21,22,23,24]
For TIF5A in maize, the phosphorylation information for S2 and S4 from P3DB source is from a largescale paper ‘Large-scale analysis of phosphorylated proteins in maize leaf’ [35], while RLIMS-P provides additional support for Ser2 phosphorylation from a lowthroughput experiment from the article ‘Phosphorylation of maize eukaryotic translation initiation factor on Ser2 by catalytic subunit CK2’ [36]
Summary
Proteins are the link between biological information in the genome and the function of cells and organisms. PTMs are prevalent and diverse (>620 types as cataloged in RESID [1]) and offer an additional level of regulation that allows a rapid, controlled and reversible response to environmental cues [2], for example, by dynamically altering interaction partner preferences in response to stimuli. These conditional interactions can either be mediated through single modification events, or often, through coordinated modification of multiple PTM types on multiple sites [3]. A comprehensive picture of PTMs, as well as the multiple factors that control PTM enzyme activity are vital to understanding how cells function in health and disease
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