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PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae

C. Stark, T.-C. Su, A. Breitkreutz, P. Lourenco, M. Dahabieh, B.-J. Breitkreutz, M. Tyers, I. Sadowski
2010 Database: The Journal of Biological Databases and Curation  
ACKNOWLEDGMENTS The authors thank LeAnn Howe and Francis Ouellette for helpful discussions.  ...  In order to systematically document and integrate these various data types, we have developed a database of experimentally verified in vivo phosphorylation sites curated from the S. cerevisiae primary  ...  PhosphoGRID is thus the first online resource that currently focuses exclusively on experimentally defined phosphorylation sites in the budding yeast S. cerevisiae.  ... 
doi:10.1093/database/bap026 pmid:20428315 pmcid:PMC2860897 fatcat:2lmv5x7r75dchmft7hwgugzky4

The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update

I. Sadowski, B.-J. Breitkreutz, C. Stark, T.-C. Su, M. Dahabieh, S. Raithatha, W. Bernhard, R. Oughtred, K. Dolinski, K. Barreto, M. Tyers
2013 Database: The Journal of Biological Databases and Curation  
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update.  ...  PhosphoGRID is an online database that curates and houses experimentally verified in vivo phosphorylation sites in the Saccharomyces cerevisiae proteome (  ...  database of experimentally verified in vivo protein phosphorylation sites focused on the model eukaryote Saccharomyces cerevisisae (2) .  ... 
doi:10.1093/database/bat026 pmid:23674503 pmcid:PMC3653121 fatcat:owoc7slcjrhedcrl427zafbrju

The BioGRID Interaction Database: 2011 update

C. Stark, B.-J. Breitkreutz, A. Chatr-aryamontri, L. Boucher, R. Oughtred, M. S. Livstone, J. Nixon, K. Van Auken, X. Wang, X. Shi, T. Reguly, J. M. Rust (+3 others)
2010 Nucleic Acids Research  
Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana), and efforts to expand  ...  The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (  ...  This sister database currently contains 6440 experimentally verified in vivo phosphorylation sites found on 1770 proteins, as curated from 329 publications (13) .  ... 
doi:10.1093/nar/gkq1116 pmid:21071413 pmcid:PMC3013707 fatcat:5e7qa7hecfbnfj7o3dvxiw4yum

Predicting kinase substrates using conservation of local motif density

Andy C. W. Lai, Alex N. Nguyen Ba, Alan M. Moses
2012 Computer applications in the biosciences : CABIOS  
Given a known consensus, the new method (ConDens) compares the observed density of matches to a null model of evolution and does not require labeled training data.  ...  Motivation: Protein kinases represent critical links in cell signaling. A central problem in computational biology is to systematically identify their substrates.  ...  For validation, experimentally verified substrates from PhosphoGRID (Stark et al., 2010) and Kinase Interaction Database (KID) (Sharifpoor et al., 2011) were selected as 'known kinase targets'.  ... 
doi:10.1093/bioinformatics/bts060 pmid:22302575 fatcat:fdkukmduvrao3dhfhcjfjiv33y

The transcription factor Swi4 is target for PKA regulation of cell size at the G1 to S transition in Saccharomyces cerevisiae

Loredana Amigoni, Sonia Colombo, Fiorella Belotti, Lilia Alberghina, Enzo Martegani
2015 Cell Cycle  
We generated a SWI4 allele mutated in the consensus site for PKA (Swi4 S159A ) and we found that expression of Swi4 S159A protein in the GG104-Swi4D strain did not restore the transient G 1 arrest induced  ...  To investigate the specific target of PKA in the regulation of cell cycle progression and cell size we developed a new approach using the yeast strain GG104 bearing a deletion in adenylate cyclase gene  ...  Supplemental Material Supplemental data for this article can be accessed on the publisher's website.  ... 
doi:10.1080/15384101.2015.1055997 pmid:26046481 pmcid:PMC4614678 fatcat:uyup2nflobabdeyzjobz5khh6m

Cks confers specificity to phosphorylation-dependent CDK signaling pathways

Denise A McGrath, Eva Rose M Balog, Mardo Kõivomägi, Rafael Lucena, Michelle V Mai, Alexander Hirschi, Douglas R Kellogg, Mart Loog, Seth M Rubin
2013 Nature Structural & Molecular Biology  
We observe that budding-yeast Cks associates with select phosphorylated sequences in cell cycle-regulatory proteins.  ...  We characterize new Cks-binding sites in the mitotic regulator Wee1 and discover a new role for Cks in regulating CDK activity at mitotic entry.  ...  identified as phosphorylation sites in the PhosphoGRID database (  ... 
doi:10.1038/nsmb.2707 pmid:24186063 pmcid:PMC4242096 fatcat:vzqmcnkhyfcobphg75q7fgktpe

In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome [article]

Michael C Lanz, Kumar Yugandhar, Shagun Gupta, Ethan Sanford, Vitor Faça, Stephanie Vega, Aaron Joiner, Chris Fromme, Haiyuan Yu, Marcus B. Smolka
2019 bioRxiv   pre-print
This single dataset nearly doubles the size of the known phosphoproteome in budding yeast and defines a set of cell cycle-regulated phosphorylation events.  ...  Phosphorylation site mutants experimentally validate our predictions and support a role for phosphorylation in negatively regulating protein-protein interactions.  ...  In recent years, the primary repository for experimentally verified phosphorylation sites in budding yeast has been BioGRID, which contains nearly 20,000 annotated phosphosites (previously known as PhosphoGRID  ... 
doi:10.1101/700070 fatcat:ite6lugnuvgrbnazrhjsdztweq

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

Kai-Yao Huang, Hsin-Yi Wu, Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Yun-Chung Hsieh, Chih-Ming Tsai, Kuo-I Lin, Hsien-Da Huang, Tzong-Yi Lee, Yu-Ju Chen
2014 Database: The Journal of Biological Databases and Curation  
The experimentally validated phosphorylation sites as well as their catalytic kinases were extracted from public resources, and MS/MS phosphopeptides were manually curated from research articles.  ...  Owing to an increasing number of in vivo phosphorylation sites that have been identified by mass spectrometry (MS)-based proteomics, the RegPhos, available online at  ...  Additionally, the PhosphoGRID (10) is a new database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae.  ... 
doi:10.1093/database/bau034 pmid:24771658 pmcid:PMC3999940 fatcat:ypjbx5ikcjb6vfdxcee35wnpna

Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates

Evgeny Kanshin, Sébastien Giguère, Cheng Jing, Mike Tyers, Pierre Thibault
2017 Molecular & Cellular Proteomics  
We applied this method to identify many direct targets of Cdc28 and Snf1 kinases in the budding yeast Saccharomyces cerevisiae.  ...  Evgeny Kanshin ‡, Sé bastien Giguè re ‡, Cheng Jing ‡, Mike Tyers ‡ §ʈ, and Pierre Thibault ‡ ¶ʈ Mass spectrometry allows quantification of tens of thousands of phosphorylation sites from minute amounts  ...  Acknowledgments-The Institute for Research in Immunology and Cancer receives infrastructure support from the Canadian Center of Excellence in Commercialization and Research, the Canadian Foundation for  ... 
doi:10.1074/mcp.m116.066233 pmid:28265048 pmcid:PMC5417821 fatcat:bomk3sbdmrguzhefn6bbw6ppoq

Phosphorylation of Sli15 by Ipl1 Is Important for Proper CPC Localization and Chromosome Stability in Saccharomyces cerevisiae

Vasso Makrantoni, Stephen J. Corbishley, Najma Rachidi, Nicholas A. Morrice, David A. Robinson, Michael J. R. Stark, Barbara G. Mellone
2014 PLoS ONE  
The chromosomal passenger complex (CPC) is a key regulator of eukaryotic cell division, consisting of the protein kinase Aurora B/Ipl1 in association with its activator (INCENP/Sli15) and two additional  ...  Instead, we find that mimicking constitutive phosphorylation of Sli15 on the Ipl1 phosphorylation sites causes delocalization of the CPC in metaphase, whereas blocking phosphorylation of Sli15 on the Ipl1  ...  Acknowledgments Thanks are due to David Campbell for help with phosphorylation site mapping, to Carol Mackintosh for providing microcystin, to Tom Owen-Hughes for providing H3.3, to Gislene Pereira and  ... 
doi:10.1371/journal.pone.0089399 pmid:24558497 pmcid:PMC3928436 fatcat:37uzwyvhozh3xnnoak7p66pqou

Gene dosage screens in yeast reveal core signalling pathways controlling heat adaptation [article]

Cosimo Jann, Andreas Johansson, Justin D Smith, Leopold Parts, Lars M Steinmetz
2020 bioRxiv   pre-print
Here we employ CRISPRi/a to down- or upregulate protein kinases and transcription factors in S. cerevisiae.  ...  The integration of these phenotypes allowed us to identify core signalling pathways of heat adaptation and reveal novel functions for the high osmolarity glycerol, unfolded protein response and protein  ...  Phosphorylation targets of protein 554 kinases were determined using the phosphogrid 2.0 database 83 .  ... 
doi:10.1101/2020.08.26.267674 fatcat:ajbdkun3hncqpoo3ainlr4qzni

Bioinformatics analysis, management and organization of biological data related to post-translational regulation [article]

Παναγιώτης Βλασταρίδης, University Of Thessaly, Γρηγόριος Αμούτζιας
Statistical analyses of the gathered and filtered data allowed for a reliable estimate of the total number of phosphoproteins and phosphorylation sites in model eukaryotes.  ...  Furthermore, a focused and in-depth study of the yeast phosphoproteome revealed its pivotal role in the central metabolism and further identified key metabolic processes of biotechnological importance  ...  Therefore, a compendium of confident protein phosphorylation sites (p-sites) for the model organism Saccharomyces cerevisiae has been analyzed.  ... 
doi:10.26253/heal.uth.9848 fatcat:27whus2kxbhrpinmchrj2aev7e

Regulation of pheromone response in saccharomyces by Ste12-PRE interaction and TOR-Cdc55 signaling

Ting-Cheng Su
Cdc55 directly or indirectly alters the phosphorylation status of Ste12, as I observed hyperphosphorylated Ste12 in the cdc55 mutant compared to wild type.  ...  Ste12 is the key regulator in the yeast pheromone response pathway and works as an important model for understanding gene regulation by MAP kinase cascades.  ...  Michael Kobor for their generous comments and advice, particularly during the preparation of this thesis.  ... 
doi:10.14288/1.0073396 fatcat:7maaazzpcbchhmz3lei35lqvmm