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iPTMnet: an integrated resource for protein post-translational modification network discovery
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—c...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753337/ https://www.ncbi.nlm.nih.gov/pubmed/29145615 http://dx.doi.org/10.1093/nar/gkx1104 |
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author | Huang, Hongzhan Arighi, Cecilia N Ross, Karen E Ren, Jia Li, Gang Chen, Sheng-Chih Wang, Qinghua Cowart, Julie Vijay-Shanker, K Wu, Cathy H |
author_facet | Huang, Hongzhan Arighi, Cecilia N Ross, Karen E Ren, Jia Li, Gang Chen, Sheng-Chih Wang, Qinghua Cowart, Julie Vijay-Shanker, K Wu, Cathy H |
author_sort | Huang, Hongzhan |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5753337 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-57533372018-01-05 iPTMnet: an integrated resource for protein post-translational modification network discovery Huang, Hongzhan Arighi, Cecilia N Ross, Karen E Ren, Jia Li, Gang Chen, Sheng-Chih Wang, Qinghua Cowart, Julie Vijay-Shanker, K Wu, Cathy H Nucleic Acids Res Database Issue 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. Oxford University Press 2018-01-04 2017-11-14 /pmc/articles/PMC5753337/ /pubmed/29145615 http://dx.doi.org/10.1093/nar/gkx1104 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Issue Huang, Hongzhan Arighi, Cecilia N Ross, Karen E Ren, Jia Li, Gang Chen, Sheng-Chih Wang, Qinghua Cowart, Julie Vijay-Shanker, K Wu, Cathy H iPTMnet: an integrated resource for protein post-translational modification network discovery |
title | iPTMnet: an integrated resource for protein post-translational modification network discovery |
title_full | iPTMnet: an integrated resource for protein post-translational modification network discovery |
title_fullStr | iPTMnet: an integrated resource for protein post-translational modification network discovery |
title_full_unstemmed | iPTMnet: an integrated resource for protein post-translational modification network discovery |
title_short | iPTMnet: an integrated resource for protein post-translational modification network discovery |
title_sort | iptmnet: an integrated resource for protein post-translational modification network discovery |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753337/ https://www.ncbi.nlm.nih.gov/pubmed/29145615 http://dx.doi.org/10.1093/nar/gkx1104 |
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