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Protocols

PhosphoGRID specifications

Information


Unique identifier OMICS_02954
Name PhosphoGRID
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes

Taxon


  • Plants and Fungi
    • Saccharomyces cerevisiae

Maintainer


  • person_outline Mike Tyers

Publications for PhosphoGRID

PhosphoGRID citations

 (9)
library_books

The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism

2017
PMCID: 5386872
PMID: 28250014
DOI: 10.1534/g3.116.037218

[…] 9% correct p-site localization (see Supplemental Material, File S1; spreadsheet: yeast p-sites). This compendium was an update of a previous yeast compendium from 12 HTP datasets (). In addition, the PhosphoGRID 2 dataset of manually curated low-throughput (LTP) p-sites (serving as a “gold standard”) () was integrated into the compendium. For comparative phosphoproteomic analyses, two datasets fro […]

call_split

Systematic Analysis of Transcriptional and Post transcriptional Regulation of Metabolism in Yeast

2017
PLoS Comput Biol
PMCID: 5224888
PMID: 28072816
DOI: 10.1371/journal.pcbi.1005297
call_split See protocol

[…] cal p-value and signed according to the direction of the enrichment, for example, regulators enriched towards negative fold-changes have a negative score. K/Ps target phosphosites were extracted from PhosphoGrid []. Specificities for a total of 177 transcription factors were collected in form of a position weight matrices (PWMs) from JASPAR []. Weight matrices were trimmed to remove consecutive st […]

library_books

Characterization of the Interaction between Rfa1 and Rad24 in Saccharomyces cerevisiae

2015
PLoS One
PMCID: 4342240
PMID: 25719602
DOI: 10.1371/journal.pone.0116512

[…] tings. All known protein interactions with Rfa1, Rfa2, or Rfa3 were obtained using BioGRID (http://www.thebiogrid.org; [,]). All currently reported phosphorylation sites for Rad24 were obtained using PhosphoGRID (http://www.phosphogrid.org; [,].Secondary structure predictions for Rad24 were obtained using Jpred3 (http://www.compbio.dundee.ac.uk/www-jpred/; [,]) and COILS (http://embnet.vital it.ch […]

library_books

TORC2 dependent protein kinase Ypk1 phosphorylates ceramide synthase to stimulate synthesis of complex sphingolipids

2014
eLife
PMCID: 4217029
PMID: 25279700
DOI: 10.7554/eLife.03779.015

[…] din A and caspifungin (all compounds that cause severe growth phenotypes in ypk1Δ strains) were identified from the literature (). Lastly, MOTIPS predicted Ypk1 phosphorylation sites were compared to Phosphogrid () to identify those sites known to be phosphorylated in vivo. To be considered a potential Ypk1 substrate in this study, a protein had to have a myriocin, aureobasidin or caspofungin phen […]

library_books

Proteomic Analyses Reveal that Sky1 Modulates Apoptosis and Mitophagy in Saccharomyces cerevisiae Cells Exposed to Cisplatin

2014
Int J Mol Sci
PMCID: 4139861
PMID: 25029545
DOI: 10.3390/ijms150712573

[…] study (with the exception of profilin and the uncharacterized protein encoded by YLR179C) are previously recognized phosphoproteins identified by conventional or phosphoproteomic analyses (data from PhosphoGrid database). However, among the identified proteins in our analyses we do not find a similar sequence to the one predicted for the Sky1 substrates, R(E/S)RSP(T/V)R; although caution about th […]

library_books

RegPhos 2.0: an updated resource to explore protein kinase–substrate phosphorylation networks in mammals

2014
PMCID: 3999940
PMID: 24771658
DOI: 10.1093/database/bau034

[…] ate experimentally verified phosphorylation sites with catalytic kinases, including Phospho.ELM (), PhosphoSitePlus (), Phosphorylation Site Database (), PHOSIDA () and PhosPhAt (). Additionally, the PhosphoGRID () is a new database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. The Phospho3D () is a database containing 3D structur […]

Citations

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PhosphoGRID institution(s)
Department of Biochemistry and Molecular Biology, Molecular Epigenetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada; Samuel Lunenfeld Research Institute, Toronto, ON, Canada; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Institute for Research in Immunology and Cancer, Universite de Montreal, Pavillon Marcelle-Coutu, Montreal, QC, Canada
PhosphoGRID funding source(s)
Supported by Grant Number 0011258 from the Canadian Cancer Society Research Institute, Grant Numbers 1R01RR024031-01 and R24RR032659 from the NIH National Center For Research Resources, Grant Number BB/F010486/1 from the Biotechnology and Biological Sciences Research Council and Grant Number HOP-120237 from the Canadian Institutes for Health Research.

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