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For: Stark C, Su TC, Breitkreutz A, Lourenco P, Dahabieh M, Breitkreutz BJ, Tyers M, Sadowski I. PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. Database (Oxford) 2010;2010:bap026. [PMID: 20428315 PMCID: PMC2860897 DOI: 10.1093/database/bap026] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 12/07/2009] [Accepted: 12/23/2009] [Indexed: 12/17/2022]
Number Cited by Other Article(s)
51
Bhandari D, Zhang J, Menon S, Lord C, Chen S, Helm JR, Thorsen K, Corbett KD, Hay JC, Ferro-Novick S. Sit4p/PP6 regulates ER-to-Golgi traffic by controlling the dephosphorylation of COPII coat subunits. Mol Biol Cell 2013;24:2727-38. [PMID: 23864707 PMCID: PMC3756924 DOI: 10.1091/mbc.e13-02-0114] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
52
Chen WM, Danziger SA, Chiang JH, Aitchison JD. PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. ACTA ACUST UNITED AC 2013;29:2435-44. [PMID: 23832245 DOI: 10.1093/bioinformatics/btt387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
53
O'Donnell AF, Huang L, Thorner J, Cyert MS. A calcineurin-dependent switch controls the trafficking function of α-arrestin Aly1/Art6. J Biol Chem 2013;288:24063-80. [PMID: 23824189 DOI: 10.1074/jbc.m113.478511] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]  Open
54
Ross KE, Arighi CN, Ren J, Huang H, Wu CH. Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013;2013:bat038. [PMID: 23749465 PMCID: PMC3675891 DOI: 10.1093/database/bat038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
55
Sadowski I, Breitkreutz BJ, Stark C, Su TC, Dahabieh M, Raithatha S, Bernhard W, Oughtred R, Dolinski K, Barreto K, Tyers M. The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013;2013:bat026. [PMID: 23674503 PMCID: PMC3653121 DOI: 10.1093/database/bat026] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
56
Pincus D, Ryan CJ, Smith RD, Brent R, Resnekov O. Assigning quantitative function to post-translational modifications reveals multiple sites of phosphorylation that tune yeast pheromone signaling output. PLoS One 2013;8:e56544. [PMID: 23554854 PMCID: PMC3595240 DOI: 10.1371/journal.pone.0056544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/15/2013] [Indexed: 12/19/2022]  Open
57
Trost B, Kusalik A. Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights. Bioinformatics 2013;29:686-94. [PMID: 23341503 DOI: 10.1093/bioinformatics/btt031] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]  Open
58
Yeast protein phosphatase 2A-Cdc55 regulates the transcriptional response to hyperosmolarity stress by regulating Msn2 and Msn4 chromatin recruitment. Mol Cell Biol 2012;33:1057-72. [PMID: 23275436 DOI: 10.1128/mcb.00834-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
59
Acker J, Conesa C, Lefebvre O. Yeast RNA polymerase III transcription factors and effectors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012;1829:283-95. [PMID: 23063749 DOI: 10.1016/j.bbagrm.2012.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/27/2012] [Accepted: 10/03/2012] [Indexed: 12/19/2022]
60
Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Systematic functional prioritization of protein posttranslational modifications. Cell 2012;150:413-25. [PMID: 22817900 DOI: 10.1016/j.cell.2012.05.036] [Citation(s) in RCA: 334] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 03/21/2012] [Accepted: 05/18/2012] [Indexed: 11/24/2022]
61
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PLoS Genet 2012;8:e1002834. [PMID: 22912585 PMCID: PMC3415404 DOI: 10.1371/journal.pgen.1002834] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 06/04/2012] [Indexed: 01/19/2023]  Open
62
Sun MGF, Sikora M, Costanzo M, Boone C, Kim PM. Network evolution: rewiring and signatures of conservation in signaling. PLoS Comput Biol 2012;8:e1002411. [PMID: 22438796 PMCID: PMC3305342 DOI: 10.1371/journal.pcbi.1002411] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 01/14/2012] [Indexed: 01/09/2023]  Open
63
Lai ACW, Nguyen Ba AN, Moses AM. Predicting kinase substrates using conservation of local motif density. ACTA ACUST UNITED AC 2012;28:962-9. [PMID: 22302575 DOI: 10.1093/bioinformatics/bts060] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
64
Amoutzias GD, He Y, Lilley KS, Van de Peer Y, Oliver SG. Evaluation and properties of the budding yeast phosphoproteome. Mol Cell Proteomics 2012;11:M111.009555. [PMID: 22286756 PMCID: PMC3433898 DOI: 10.1074/mcp.m111.009555] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
65
Sharifpoor S, van Dyk D, Costanzo M, Baryshnikova A, Friesen H, Douglas AC, Youn JY, VanderSluis B, Myers CL, Papp B, Boone C, Andrews BJ. Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. Genome Res 2012;22:791-801. [PMID: 22282571 DOI: 10.1101/gr.129213.111] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
66
Briache A, Marrakchi K, Kerzazi A, Navas-Delgado I, Rossi Hassani BD, Lairini K, Aldana-Montes JF. Transparent mediation-based access to multiple yeast data sources using an ontology driven interface. BMC Bioinformatics 2012;13 Suppl 1:S7. [PMID: 22372975 PMCID: PMC3471333 DOI: 10.1186/1471-2105-13-s1-s7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
67
Akiva E, Friedlander G, Itzhaki Z, Margalit H. A dynamic view of domain-motif interactions. PLoS Comput Biol 2012;8:e1002341. [PMID: 22253583 PMCID: PMC3257277 DOI: 10.1371/journal.pcbi.1002341] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 11/20/2011] [Indexed: 11/19/2022]  Open
68
Mass Spectrometric Tools for Systematic Analysis of Protein Phosphorylation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012;106:3-32. [DOI: 10.1016/b978-0-12-396456-4.00014-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
69
Oliveira AP, Sauer U. The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism. FEMS Yeast Res 2011;12:104-17. [DOI: 10.1111/j.1567-1364.2011.00765.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 11/30/2022]  Open
70
Mollapour M, Piper PW. Activity of the yeast zinc-finger transcription factor War1 is lost with alanine mutation of two putative phosphorylation sites in the activation domain. Yeast 2011;29:39-44. [DOI: 10.1002/yea.1915] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2011] [Accepted: 10/10/2011] [Indexed: 11/06/2022]  Open
71
Chatr-Aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M. Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. BMC Bioinformatics 2011;12 Suppl 8:S8. [PMID: 22151178 PMCID: PMC3269943 DOI: 10.1186/1471-2105-12-s8-s8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
72
Skrzypek MS, Hirschman J. Using the Saccharomyces Genome Database (SGD) for analysis of genomic information. CURRENT PROTOCOLS IN BIOINFORMATICS 2011;Chapter 1:1.20.1-1.20.23. [PMID: 21901739 PMCID: PMC3191907 DOI: 10.1002/0471250953.bi0120s35] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
73
Huber A, French SL, Tekotte H, Yerlikaya S, Stahl M, Perepelkina MP, Tyers M, Rougemont J, Beyer AL, Loewith R. Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L. EMBO J 2011;30:3052-64. [PMID: 21730963 PMCID: PMC3160192 DOI: 10.1038/emboj.2011.221] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 06/08/2011] [Indexed: 01/22/2023]  Open
74
Fasolo J, Sboner A, Sun MGF, Yu H, Chen R, Sharon D, Kim PM, Gerstein M, Snyder M. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes Dev 2011;25:767-78. [PMID: 21460040 DOI: 10.1101/gad.1998811] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
75
Xie LX, Hsieh EJ, Watanabe S, Allan CM, Chen JY, Tran UC, Clarke CF. Expression of the human atypical kinase ADCK3 rescues coenzyme Q biosynthesis and phosphorylation of Coq polypeptides in yeast coq8 mutants. BIOCHIMICA ET BIOPHYSICA ACTA 2011;1811:348-60. [PMID: 21296186 PMCID: PMC3075350 DOI: 10.1016/j.bbalip.2011.01.009] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 01/17/2011] [Accepted: 01/28/2011] [Indexed: 12/31/2022]
76
Sharifpoor S, Nguyen Ba AN, Youn JY, Young JY, van Dyk D, Friesen H, Douglas AC, Kurat CF, Chong YT, Founk K, Moses AM, Andrews BJ. A quantitative literature-curated gold standard for kinase-substrate pairs. Genome Biol 2011;12:R39. [PMID: 21492431 PMCID: PMC3218865 DOI: 10.1186/gb-2011-12-4-r39] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/09/2011] [Accepted: 04/14/2011] [Indexed: 01/05/2023]  Open
77
Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R. Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal 2010;3:rs4. [PMID: 21177495 PMCID: PMC3072779 DOI: 10.1126/scisignal.2001182] [Citation(s) in RCA: 243] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
78
Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 2010;39:D698-704. [PMID: 21071413 PMCID: PMC3013707 DOI: 10.1093/nar/gkq1116] [Citation(s) in RCA: 629] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
79
Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Phospho.ELM: a database of phosphorylation sites--update 2011. Nucleic Acids Res 2010;39:D261-7. [PMID: 21062810 PMCID: PMC3013696 DOI: 10.1093/nar/gkq1104] [Citation(s) in RCA: 472] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
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