Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

General information

Description: PhosphoSitePlus(®) (PSP), a knowledgebase dedicated to mammalian post-translational modifications (PTMs), contains over 330,000 non-redundant PTMs, including phospho, acetyl, ubiquityl and methyl groups.
Year founded: 2012
Last update: 2014-12
Version: v1.0
Accessibility:
Manual:
Accessible
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Country/Region: United States
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Cell Signaling Technology
Address: Cell Signaling Technology,3 Trask Lane,Danvers,MA 01923,USA
City: Danvers
Province/State: MA
Country/Region: United States
Contact name (PI/Team): EditorPhosphoSite
Contact email (PI/Helpdesk): EditorPhosphoSite@cellsignal.com

Record metadata

Created on: 2015-06-20
Curated by:
Dong Zou [2019-01-08]
Zhang Zhang [2015-12-31]
Shixiang Sun [2015-11-21]
Shixiang Sun [2015-06-26]

Ranking

All databases:
53/4692 (98.892%)
Modification:
4/201 (98.507%)
53
Total Rank
1,424
Citations
178
z-index

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Publications

30445427
15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms. [PMID: 30445427]
Hornbeck PV, Kornhauser JM, Latham V, Murray B, Nandhikonda V, Nord A, Skrzypek E, Wheeler T, Zhang B, Gnad F.

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.

Nucleic Acids Res. 2019:47(D1) | 14 Citations (from Europe PMC, 2020-09-12)
25514926
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. [PMID: 25514926]
Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E.

PhosphoSitePlus(®) (PSP, http://www.phosphosite.org/), a knowledgebase dedicated to mammalian post-translational modifications (PTMs), contains over 330,000 non-redundant PTMs, including phospho, acetyl, ubiquityl and methyl groups. Over 95% of the sites are from mass spectrometry (MS) experiments. In order to improve data reliability, early MS data have been reanalyzed, applying a common standard of analysis across over 1,000,000 spectra. Site assignments with P > 0.05 were filtered out. Two new downloads are available from PSP. The 'Regulatory sites' dataset includes curated information about modification sites that regulate downstream cellular processes, molecular functions and protein-protein interactions. The 'PTMVar' dataset, an intersect of missense mutations and PTMs from PSP, identifies over 25,000 PTMVars (PTMs Impacted by Variants) that can rewire signaling pathways. The PTMVar data include missense mutations from UniPROTKB, TCGA and other sources that cause over 2000 diseases or syndromes (MIM) and polymorphisms, or are associated with hundreds of cancers. PTMVars include 18 548 phosphorlyation sites, 3412 ubiquitylation sites, 2316 acetylation sites, 685 methylation sites and 245 succinylation sites. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 660 Citations (from Europe PMC, 2020-09-19)
22135298
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. [PMID: 22135298]
Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M.

PhosphoSitePlus (http://www.phosphosite.org) is an open, comprehensive, manually curated and interactive resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins. It encompasses 1,30,000 non-redundant modification sites, primarily phosphorylation, ubiquitinylation and acetylation. The interface is designed for clarity and ease of navigation. From the home page, users can launch simple or complex searches and browse high-throughput data sets by disease, tissue or cell line. Searches can be restricted by specific treatments, protein types, domains, cellular components, disease, cell types, cell lines, tissue and sequences or motifs. A few clicks of the mouse will take users to substrate pages or protein pages with sites, sequences, domain diagrams and molecular visualization of side-chains known to be modified; to site pages with information about how the modified site relates to the functions of specific proteins and cellular processes and to curated information pages summarizing the details from one record. PyMOL and Chimera scripts that colorize reactive groups on residues that are modified can be downloaded. Features designed to facilitate proteomic analyses include downloads of modification sites, kinase-substrate data sets, sequence logo generators, a Cytoscape plugin and BioPAX download to enable pathway visualization of the kinase-substrate interactions in PhosphoSitePlus®.

Nucleic Acids Res. 2012:40(Database issue) | 750 Citations (from Europe PMC, 2020-09-19)