Cargando…

15 years of PhosphoSitePlus(®): integrating post-translationally modified sites, disease variants and isoforms

For 15 years the mission of PhosphoSitePlus(®) (PSP, https://www.phosphosite.org) has been to provide comprehensive information and tools for the study of mammalian post-translational modifications (PTMs). The number of unique PTMs in PSP is now more than 450 000 from over 22 000 articles and thousa...

Descripción completa

Detalles Bibliográficos
Autores principales: Hornbeck, Peter V, Kornhauser, Jon M, Latham, Vaughan, Murray, Beth, Nandhikonda, Vidhisha, Nord, Alex, Skrzypek, Elżbieta, Wheeler, Travis, Zhang, Bin, Gnad, Florian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324072/
https://www.ncbi.nlm.nih.gov/pubmed/30445427
http://dx.doi.org/10.1093/nar/gky1159
_version_ 1783385905005854720
author Hornbeck, Peter V
Kornhauser, Jon M
Latham, Vaughan
Murray, Beth
Nandhikonda, Vidhisha
Nord, Alex
Skrzypek, Elżbieta
Wheeler, Travis
Zhang, Bin
Gnad, Florian
author_facet Hornbeck, Peter V
Kornhauser, Jon M
Latham, Vaughan
Murray, Beth
Nandhikonda, Vidhisha
Nord, Alex
Skrzypek, Elżbieta
Wheeler, Travis
Zhang, Bin
Gnad, Florian
author_sort Hornbeck, Peter V
collection PubMed
description For 15 years the mission of PhosphoSitePlus(®) (PSP, https://www.phosphosite.org) has been to provide comprehensive information and tools for the study of mammalian post-translational modifications (PTMs). The number of unique PTMs in PSP is now more than 450 000 from over 22 000 articles and thousands of MS datasets. The most important areas of growth in PSP are in disease and isoform informatics. Germline mutations associated with inherited diseases and somatic cancer mutations have been added to the database and can now be viewed along with PTMs and associated quantitative information on novel ‘lollipop' plots. These plots enable researchers to interactively visualize the overlap between disease variants and PTMs, and to identify mutations that may alter phenotypes by rewiring signaling networks. We are expanding the sequence space to include over 30 000 human and mouse isoforms to enable researchers to explore the important but understudied biology of isoforms. This represents a necessary expansion of sequence space to accommodate the growing precision and depth of coverage enabled by ongoing advances in mass spectrometry. Isoforms are aligned using a new algorithm. Exploring the worlds of PTMs and disease mutations in the entire isoform space will hopefully lead to new biomarkers, therapeutic targets, and insights into isoform biology.
format Online
Article
Text
id pubmed-6324072
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-63240722019-01-10 15 years of PhosphoSitePlus(®): integrating post-translationally modified sites, disease variants and isoforms Hornbeck, Peter V Kornhauser, Jon M Latham, Vaughan Murray, Beth Nandhikonda, Vidhisha Nord, Alex Skrzypek, Elżbieta Wheeler, Travis Zhang, Bin Gnad, Florian Nucleic Acids Res Database Issue For 15 years the mission of PhosphoSitePlus(®) (PSP, https://www.phosphosite.org) has been to provide comprehensive information and tools for the study of mammalian post-translational modifications (PTMs). The number of unique PTMs in PSP is now more than 450 000 from over 22 000 articles and thousands of MS datasets. The most important areas of growth in PSP are in disease and isoform informatics. Germline mutations associated with inherited diseases and somatic cancer mutations have been added to the database and can now be viewed along with PTMs and associated quantitative information on novel ‘lollipop' plots. These plots enable researchers to interactively visualize the overlap between disease variants and PTMs, and to identify mutations that may alter phenotypes by rewiring signaling networks. We are expanding the sequence space to include over 30 000 human and mouse isoforms to enable researchers to explore the important but understudied biology of isoforms. This represents a necessary expansion of sequence space to accommodate the growing precision and depth of coverage enabled by ongoing advances in mass spectrometry. Isoforms are aligned using a new algorithm. Exploring the worlds of PTMs and disease mutations in the entire isoform space will hopefully lead to new biomarkers, therapeutic targets, and insights into isoform biology. Oxford University Press 2019-01-08 2018-11-16 /pmc/articles/PMC6324072/ /pubmed/30445427 http://dx.doi.org/10.1093/nar/gky1159 Text en © The Author(s) 2018. 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
Hornbeck, Peter V
Kornhauser, Jon M
Latham, Vaughan
Murray, Beth
Nandhikonda, Vidhisha
Nord, Alex
Skrzypek, Elżbieta
Wheeler, Travis
Zhang, Bin
Gnad, Florian
15 years of PhosphoSitePlus(®): integrating post-translationally modified sites, disease variants and isoforms
title 15 years of PhosphoSitePlus(®): integrating post-translationally modified sites, disease variants and isoforms
title_full 15 years of PhosphoSitePlus(®): integrating post-translationally modified sites, disease variants and isoforms
title_fullStr 15 years of PhosphoSitePlus(®): integrating post-translationally modified sites, disease variants and isoforms
title_full_unstemmed 15 years of PhosphoSitePlus(®): integrating post-translationally modified sites, disease variants and isoforms
title_short 15 years of PhosphoSitePlus(®): integrating post-translationally modified sites, disease variants and isoforms
title_sort 15 years of phosphositeplus(®): integrating post-translationally modified sites, disease variants and isoforms
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324072/
https://www.ncbi.nlm.nih.gov/pubmed/30445427
http://dx.doi.org/10.1093/nar/gky1159
work_keys_str_mv AT hornbeckpeterv 15yearsofphosphositeplusintegratingposttranslationallymodifiedsitesdiseasevariantsandisoforms
AT kornhauserjonm 15yearsofphosphositeplusintegratingposttranslationallymodifiedsitesdiseasevariantsandisoforms
AT lathamvaughan 15yearsofphosphositeplusintegratingposttranslationallymodifiedsitesdiseasevariantsandisoforms
AT murraybeth 15yearsofphosphositeplusintegratingposttranslationallymodifiedsitesdiseasevariantsandisoforms
AT nandhikondavidhisha 15yearsofphosphositeplusintegratingposttranslationallymodifiedsitesdiseasevariantsandisoforms
AT nordalex 15yearsofphosphositeplusintegratingposttranslationallymodifiedsitesdiseasevariantsandisoforms
AT skrzypekelzbieta 15yearsofphosphositeplusintegratingposttranslationallymodifiedsitesdiseasevariantsandisoforms
AT wheelertravis 15yearsofphosphositeplusintegratingposttranslationallymodifiedsitesdiseasevariantsandisoforms
AT zhangbin 15yearsofphosphositeplusintegratingposttranslationallymodifiedsitesdiseasevariantsandisoforms
AT gnadflorian 15yearsofphosphositeplusintegratingposttranslationallymodifiedsitesdiseasevariantsandisoforms