iPTMnet


29145615	iPTMnet: an integrated resource for protein post-translational modification network discovery. [PMID: 29145615] Huang H, Arighi CN, Ross KE, Ren J, Li G, Chen SC, Wang Q, Cowart J, Vijay-Shanker K, Wu CH. 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. Nucleic Acids Res. 2018:46(D1) \| 79 Citations (from Europe PMC, 2025-03-22)

iPTMnet: an integrated resource for protein post-translational modification network discovery. [PMID: 29145615]

Huang H, Arighi CN, Ross KE, Ren J, Li G, Chen SC, Wang Q, Cowart J, Vijay-Shanker K, Wu CH.

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.

Nucleic Acids Res. 2018:46(D1) | 79 Citations (from Europe PMC, 2025-03-22)

URL:	https://research.bioinformatics.udel.edu/iptmnet/
Full name:	a approach for PTM knowledge discovery
Description:	Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. iPTMnet is developed 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.
Year founded:	2018
Last update:
Version:
Accessibility:	Accessible
Country/Region:	United States

Data type:	Protein
Data object:	Animal Fungi Plant
Database category:	Modification
Major species:	Homo sapiens Mus musculus Rattus norvegicus Saccharomyces cerevisiae Drosophila melanogaster Caenorhabditis elegans Arabidopsis thaliana Zea mays Oryza sativa
Keywords:	post-translational modifications

University/Institution:	University of Delaware
Address:
City:
Province/State:
Country/Region:	United States
Contact name (PI/Team):	Hongzhan Huang
Contact email (PI/Helpdesk):	ude.ledu.ibd@gnauh

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Database Commons a catalog of worldwide biological databases