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Protocols

Phospho.ELM specifications

Information


Unique identifier OMICS_02423
Name Phospho.ELM
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Version 9.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Phospho.ELM

Maintainers


  • person_outline Toby J. Gibson
  • person_outline Francesca Diella
  • person_outline Phospho.ELM Team

Publications for Phospho.ELM

Phospho.ELM citations

 (69)
library_books

A validated antibody panel for the characterization of tau post translational modifications

2017
Mol Neurodegener
PMCID: 5697095
PMID: 29157277
DOI: 10.1186/s13024-017-0229-1

[…] Initially, tau PTMs were retrieved from the dbPTM database, which combines experimentally validated PTM sites from a number of resources including the Human Protein Reference Database (HPRD 9.0), the Phospho.ELM database (PhosphoELM.10011), PhosphoSitePlus (Phosphositeplus.1010730), UniProtKB/Swiss-Prot (Phosphositeplus.1010730), and SysPTM (SysPTM 1.1). We used the Uniprot ID: P10636 to query dbP […]

call_split

A Novel Phosphorylation Site Kinase Network Based Method for the Accurate Prediction of Kinase Substrate Relationships

2017
Biomed Res Int
PMCID: 5660750
PMID: 29312990
DOI: 10.1155/2017/1826496
call_split See protocol

[…] s study, we employ an experimentally verified human phosphorylation sites with corresponding kinases dataset, which include 6,839 verified sites and 389 kinases with 9,480 known ssKSRs extracted from Phospho.ELM [] and the latest PhosphoSitePlus []. And, for this dataset, we follow Xu et al. [] and Wang et al. [] and use BlastClust with 70% threshold to remove substrate redundancy. Since iGPS [], […]

library_books

BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery

2017
Nucleic Acids Res
PMCID: 5753215
DOI: 10.1093/nar/gkx907

[…] pping of UniProtKB feature (FT) lines (see for a list of all FT entities used in functional annotations). Additional sources of functional annotations include: CDD (), SysPTM 1.1 (), PhosphoSite (), Phospho.ELM (), dbSNO 1.0 (), HPRD 9.0 () and OGlycBase6.0 ().Finally, all variation entries were unified to Disease Ontology or DO () terms to facilitate better cancer classification and easier datab […]

library_books

Petri Net Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma

2017
Front Microbiol
PMCID: 5592237
PMID: 28932213
DOI: 10.3389/fmicb.2017.01682

[…] (Wong et al., ), and GPS 2.1 (Xue et al., ). Sites verified by two or more databases were selected. Obtained results were then scanned manually for experimentally verified sites within literature and Phospho. ELM database (Diella et al., ) was also consulted to identify experimentally validated phosphorylation sites. To prioritize sites exposed (Surface accessibility) for kinases NetSurfP (Peterse […]

library_books

Phosphoproteomic Analysis Reveals the Importance of Kinase Regulation During Orbivirus Infection*

2017
PMCID: 5672004
PMID: 28851738
DOI: 10.1074/mcp.M117.067355

[…] ds) and mean log2 ratios were uploaded to the software. Phoxtrack was set to require a minimum of two phosphosites per kinase, and 10,000 permutations. The human PhosphoSitePlus, SWISS-Prot, HPRD and Phospho.ELM were selected as the databases for screening. Phoxtrack kinase and substrate analysis are shown in supplemental Table S7. […]

library_books

Systematic identification of phosphorylation mediated protein interaction switches

2017
PLoS Comput Biol
PMCID: 5386296
PMID: 28346509
DOI: 10.1371/journal.pcbi.1005462

[…] sculus, D. melanogaster, C. elegans, S. cerevisae) from a previous study [] and identified 258,552 phosphosites in PhosphoSitePlus [], UniProt [] (those with experimental evidence only), dbPTM [] and phospho.ELM []. We also extracted phosphorylated Serine, Threonine and Tyrosine residues within known 3D structures [] which we mapped to UniProt sequences through MUSCLE [] sequence alignments of SIF […]

Citations

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Phospho.ELM institution(s)
SCB Unit, EMBL Heidelberg, Heidelberg, Germany; Genoscope (CEA - Institut de Genomique), Evry, France; Biocomputing group, Department of Biochemical Science ‘‘A. Rossi Fanelli’’, Sapienza University of Rome, Rome, Italy; Victorian Centre for Functional Genomics, Peter MacCallum Cancer Center, East Melbourne, VIC, Australia; NNF Center for Protein Research, Faculty of Health Sciences, Copenhagen, Denmark; Biobyte solutions GmbH, Heidelberg, Germany

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