PhosphoSitePlus, 2014: mutations, PTMs and recalibrations
Top Cited Papers
Open Access
- 16 December 2014
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 43 (D1), D512-D520
- https://doi.org/10.1093/nar/gku1267
Abstract
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.Keywords
This publication has 31 references indexed in Scilit:
- A probability-based approach for high-throughput protein phosphorylation analysis and site localizationNature Biotechnology, 2006
- Two Sample Logo: a graphical representation of the differences between two sets of sequence alignmentsBioinformatics, 2006
- The Universal Protein Resource (UniProt): an expanding universe of protein informationNucleic Acids Research, 2006
- Comparative PRKAR1A genotype–phenotype analyses in humans with Carney complex and prkar1a haploinsufficient miceProceedings of the National Academy of Sciences, 2004
- The importance of intrinsic disorder for protein phosphorylationNucleic Acids Research, 2004
- Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifsNucleic Acids Research, 2003
- Phosphorylation and Mutations of Ser16 in Human Phenylalanine HydroxylasePublished by Elsevier BV ,2002
- Occurrence of NKX3.1 C154T polymorphism in men with and without prostate cancer and studies of its effect on protein function.2002
- The Wilhelmine E. Key 2001 Invitational Lecture. Estimation of Divergence Times for a Few Mammalian and Several Primate SpeciesJournal of Heredity, 2002
- Allelic and locus heterogeneity in inherited venous malformationsHuman Molecular Genetics, 1999