PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

By P. Hornbeck, Bin Zhang, Beth Murray, J. Kornhauser, V. Latham, E. Skrzypek. 2014

2,997 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy

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Citations in the corpus

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding (2018, background): “Integration with the UniProt resource enables the display of various additional information about the requested protein (when available), such as PFAM annotations (47), low-throughput post-translational modifications (including phosphorylation, methylation and acetylation sites) from PhosphoSitePlus”
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma (2019, methodology): “A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript REAGENT or RESOURCE SOURCE IDENTIFIER TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold Illumina Catalog: RS-122-2301 Infinium MethylationEPIC Kit Illumina Catalog: WG-317-1003 Nextera DNA Exosome Kit Illumi”
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis (2020, neutral): “We think this illustrates well the impact that dedicated application papers can achieve by using OmniPath.”
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins (2016, neutral): “PhosphoSitePlus Phosphosite-Disease Associations (63, 64)”
WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs (2019, background): “Although the increase in numbers mainly results from updates to upstream data sources, a few new databases were added in WebGestalt 2019 (Table 1), including a cancer-related subset of WikiPathways (7), co-expression network modules derived from cancer proteomics datasets from CPTAC (Clinical Proteo”
Pi-Pi contacts are an overlooked protein feature relevant to phase separation (2018, methodology): “…(Magrane et al., 2011; Pundir et al., 2017; Huntley et al., 2015; Suzek et al., 2007), PTM data from PhosphoSitePlus (release Dec-16–2011) (Hornbeck et al., 2015), human protein-protein interactions collated under the Interologous Interactions Database (I2D) (version 2.9) (Brown and…”
Towards a structurally resolved human protein interaction network (2021, background): “Over 100,000 experimental human phosphorylation sites have been determined to date 26,27 , but only 5–10% of these have a known function 28 .”
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation (2021, background): “Low-throughput post-translational modifications (including Ser, Thr and His phosphorylations, methylation, ubiquitylation and acetylation sites) from PhosphoSitePlus (38) are also indicated.”
Pathogenic germline variants in 10,389 adult cancers (2018, methodology): “, 2018), PhosphoSitePlus (Hornbeck et al., 2015) and UniProt Knowledge Base (The UniProt Consortium, 2017).”