{ "bcoid": "GLY_000803", "title": "Yeast Proteoform Phosphorylation Citations (iPTMnet)", "description": "", "filename": "yeast_proteoform_citations_phosphorylation_sites_iptmnet.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Proteoform" ], "tag": [ "Phosphorylation Citations (iPTMnet)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P04050-1...", "Pol II CTD k..." ], [ "P14737-1...", "Dpb11 coordi..." ] ], "headers": [ "uniprotkb_ca...", "title..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "title" }, { "type": "string", "label": "journal_name" }, { "type": "string", "label": "publication_date" }, { "type": "string", "label": "authors" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" } ], [ "P04050-1", "Pol II CTD kinases Bur1 and Kin28 promote Spt5 CTR-independent recruitment of Paf1 complex.", "The EMBO journal", "2012-08-15", "Qiu Hongfang, Hu Cuihua, Gaur Naseem A, Hinnebusch Alan G", "protein_xref_pubmed", "22796944", "protein_xref_iptmnet", "P04050" ], [ "P14737-1", "Dpb11 coordinates Mec1 kinase activation with cell cycle-regulated Rad9 recruitment.", "The EMBO journal", "2011-09-23", "Pfander Boris, Diffley John F X", "protein_xref_pubmed", "21946560", "protein_xref_iptmnet", "P14737" ], [ "P27692-1", "Pol II CTD kinases Bur1 and Kin28 promote Spt5 CTR-independent recruitment of Paf1 complex.", "The EMBO journal", "2012-08-15", "Qiu Hongfang, Hu Cuihua, Gaur Naseem A, Hinnebusch Alan G", "protein_xref_pubmed", "22796944", "protein_xref_iptmnet", "P27692" ], [ "P32356-1", "Role of 14-3-3 proteins in the regulation of neutral trehalase in the yeast Saccharomyces cerevisiae.", "FEMS yeast research", "2008-02", "Panni Simona, Landgraf Christiane, Volkmer-Engert Rudolf, Cesareni Gianni, Castagnoli Luisa", "protein_xref_pubmed", "17916074", "protein_xref_iptmnet", "P32356" ], [ "P34244-1", "Phosphorylation of Hsl1 by Hog1 leads to a G2 arrest essential for cell survival at high osmolarity.", "The EMBO journal", "2006-06-07", "Clotet Josep, Escot\u00e9 Xavier, Adrover Miquel Angel, Yaakov Gilad, Gar\u00ed Eloi, Aldea Mart\u00ed, de Nadal Eul\u00e0lia, Posas Francesc", "protein_xref_pubmed", "16688223", "protein_xref_iptmnet", "P34244" ], [ "P35187-1", "An N-terminal acidic region of Sgs1 interacts with Rpa70 and recruits Rad53 kinase to stalled forks.", "The EMBO journal", "2012-09-12", "Hegnauer Anna Maria, Hustedt Nicole, Shimada Kenji, Pike Brietta L, Vogel Markus, Amsler Philipp, Rubin Seth M, van Leeuwen Fred, Gu\u00e9nol\u00e9 Aude, van Attikum Haico, Thom\u00e4 Nicolas H, Gasser Susan M", "protein_xref_pubmed", "22820947", "protein_xref_iptmnet", "P35187" ], [ "P38634-1", "Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor.", "Proceedings of the National Academy of Sciences of the United States of America", "2008-11-18", "Mittag Tanja, Orlicky Stephen, Choy Wing-Yiu, Tang Xiaojing, Lin Hong, Sicheri Frank, Kay Lewis E, Tyers Mike, Forman-Kay Julie D", "protein_xref_pubmed", "19008353", "protein_xref_iptmnet", "P38634" ], [ "P43601-1", "DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1.", "The EMBO journal", "2012-04-04", "Travesa Anna, Kuo Dwight, de Bruin Robertus A M, Kalashnikova Tatyana I, Guaderrama Marisela, Thai Kevin, Aslanian Aaron, Smolka Marcus B, Yates John R, Ideker Trey, Wittenberg Curt", "protein_xref_pubmed", "22333915", "protein_xref_iptmnet", "P43601" ], [ "P53135-1", "Dpb11 coordinates Mec1 kinase activation with cell cycle-regulated Rad9 recruitment.", "The EMBO journal", "2011-09-23", "Pfander Boris, Diffley John F X", "protein_xref_pubmed", "21946560", "protein_xref_iptmnet", "P53135" ], [ "P06738-1", "Purification and crystallization of glycogen phosphorylase from Saccharomyces cerevisiae.", "Journal of molecular biology", "1992-06-20", "Rath V L, Hwang P K, Fletterick R J", "protein_xref_pubmed", "1613787", "protein_xref_iptmnet", "P06738" ], [ "P06782-1", "Mammalian AMP-activated protein kinase shares structural and functional homology with the catalytic domain of yeast Snf1 protein kinase.", "The Journal of biological chemistry", "1994 Jan 28", "Mitchelhill KI, Stapleton D, Gao G, House C, Michell B, Katsis F, Witters LA, Kemp BE", "protein_xref_pubmed", "7905477", "protein_xref_iptmnet", "P06782" ], [ "P06784-1", "Activation of MEK family kinases requires phosphorylation of two conserved Ser/Thr residues.", "The EMBO journal", "1994 Mar 1", "Zheng CF, Guan KL", "protein_xref_pubmed", "8131746", "protein_xref_iptmnet", "P06784" ], [ "P06786-1", "Topoisomerase II: its functions and phosphorylation.", "Antonie van Leeuwenhoek", "1992-08", "Gasser S M, Walter R, Dang Q, Cardenas M E", "protein_xref_pubmed", "1332607", "protein_xref_iptmnet", "P06786" ], [ "P07248-1", "Isoform-specific purification and substrate specificity of the 5'-AMP-activated protein kinase.", "The Journal of biological chemistry", "1996-11-08", "Michell B J, Stapleton D, Mitchelhill K I, House C M, Katsis F, Witters L A, Kemp B E", "protein_xref_pubmed", "8910470", "protein_xref_iptmnet", "P07248" ], [ "P07248-1", "Cyclic AMP-dependent protein kinase phosphorylates and inactivates the yeast transcriptional activator ADR1.", "Cell", "1989-02-10", "Cherry J R, Johnson T R, Dollard C, Shuster J R, Denis C L", "protein_xref_pubmed", "2644045", "protein_xref_iptmnet", "P07248" ], [ "P07260-1", "Characterization of the in vivo phosphorylation sites of the mRNA.cap-binding complex proteins eukaryotic initiation factor-4E and p20 in Saccharomyces cerevisiae.", "The Journal of biological chemistry", "1995-11-03", "Zanchin N I, McCarthy J E", "protein_xref_pubmed", "7592868", "protein_xref_iptmnet", "P07260" ], [ "P07278-1", "Protein kinase phosphorylation site sequences and consensus specificity motifs: tabulations.", "Methods in enzymology", "1991", "Pearson RB, Kemp BE", "protein_xref_pubmed", "1956339", "protein_xref_iptmnet", "P07278" ], [ "P08153-1", "The role of phosphorylation and the CDC28 protein kinase in cell cycle-regulated nuclear import of the S. cerevisiae transcription factor SWI5.", "Cell", "1991-08-23", "Moll T, Tebb G, Surana U, Robitsch H, Nasmyth K", "protein_xref_pubmed", "1652372", "protein_xref_iptmnet", "P08153" ], [ "P09201-1", "Amino acid sequence of the phosphorylation site of yeast (Saccharomyces cerevisiae) fructose-1,6-bisphosphatase.", "The Journal of biological chemistry", "1986-03-25", "Rittenhouse J, Harrsch P B, Kim J N, Marcus F", "protein_xref_pubmed", "3005313", "protein_xref_iptmnet", "P09201" ], [ "P12962-1", "Characterization of the in vivo phosphorylation sites of the mRNA.cap-binding complex proteins eukaryotic initiation factor-4E and p20 in Saccharomyces cerevisiae.", "The Journal of biological chemistry", "1995-11-03", "Zanchin N I, McCarthy J E", "protein_xref_pubmed", "7592868", "protein_xref_iptmnet", "P12962" ], [ "P14164-1", "The multifunctional protein OBF1 is phosphorylated at serine and threonine residues in Saccharomyces cerevisiae.", "Proceedings of the National Academy of Sciences of the United States of America", "1991-05-15", "Francesconi S C, Eisenberg S", "protein_xref_pubmed", "2034654", "protein_xref_iptmnet", "P14164" ], [ "P14164-1", "ABF1 Ser-720 is a predominant phosphorylation site for casein kinase II of Saccharomyces cerevisiae.", "The Journal of biological chemistry", "1995-07-07", "Upton T, Wiltshire S, Francesconi S, Eisenberg S", "protein_xref_pubmed", "7608180", "protein_xref_iptmnet", "P14164" ], [ "P14681-1", "Signal transduction in Saccharomyces cerevisiae requires tyrosine and threonine phosphorylation of FUS3 and KSS1.", "Genes & development", "1992-07", "Gartner A, Nasmyth K, Ammerer G", "protein_xref_pubmed", "1628831", "protein_xref_iptmnet", "P14681" ], [ "P16892-1", "Signal transduction in Saccharomyces cerevisiae requires tyrosine and threonine phosphorylation of FUS3 and KSS1.", "Genes & development", "1992-07", "Gartner A, Nasmyth K, Ammerer G", "protein_xref_pubmed", "1628831", "protein_xref_iptmnet", "P16892" ], [ "P23301-1", "Translation initiation factor eIF-5A, the hypusine-containing protein, is phosphorylated on serine in Saccharomyces cerevisiae.", "The Journal of biological chemistry", "1993-07-15", "Kang H A, Schwelberger H G, Hershey J W", "protein_xref_pubmed", "8325852", "protein_xref_iptmnet", "P23301" ], [ "P35734-1", "Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p.", "Cell", "2002 Oct 18", "Cheeseman IM, Anderson S, Jwa M, Green EM, Kang Js, Yates JR 3rd, Chan CS, Drubin DG, Barnes G", "protein_xref_pubmed", "12408861", "protein_xref_iptmnet", "P35734" ], [ "P35734-1", "Aurora kinases link chromosome segregation and cell division to cancer susceptibility.", "Current opinion in genetics & development", "2004 Feb", "Meraldi P, Honda R, Nigg EA", "protein_xref_pubmed", "15108802", "protein_xref_iptmnet", "P35734" ], [ "P36131-1", "Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p.", "Cell", "2002 Oct 18", "Cheeseman IM, Anderson S, Jwa M, Green EM, Kang Js, Yates JR 3rd, Chan CS, Drubin DG, Barnes G", "protein_xref_pubmed", "12408861", "protein_xref_iptmnet", "P36131" ], [ "P36131-1", "Aurora kinases link chromosome segregation and cell division to cancer susceptibility.", "Current opinion in genetics & development", "2004 Feb", "Meraldi P, Honda R, Nigg EA", "protein_xref_pubmed", "15108802", "protein_xref_iptmnet", "P36131" ], [ "P38283-1", "Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p.", "Cell", "2002 Oct 18", "Cheeseman IM, Anderson S, Jwa M, Green EM, Kang Js, Yates JR 3rd, Chan CS, Drubin DG, Barnes G", "protein_xref_pubmed", "12408861", "protein_xref_iptmnet", "P38283" ], [ "P38991-1", "Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p.", "Cell", "2002 Oct 18", "Cheeseman IM, Anderson S, Jwa M, Green EM, Kang Js, Yates JR 3rd, Chan CS, Drubin DG, Barnes G", "protein_xref_pubmed", "12408861", "protein_xref_iptmnet", "P38991" ], [ "P40460-1", "Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p.", "Cell", "2002 Oct 18", "Cheeseman IM, Anderson S, Jwa M, Green EM, Kang Js, Yates JR 3rd, Chan CS, Drubin DG, Barnes G", "protein_xref_pubmed", "12408861", "protein_xref_iptmnet", "P40460" ], [ "P53267-1", "Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p.", "Cell", "2002 Oct 18", "Cheeseman IM, Anderson S, Jwa M, Green EM, Kang Js, Yates JR 3rd, Chan CS, Drubin DG, Barnes G", "protein_xref_pubmed", "12408861", "protein_xref_iptmnet", "P53267" ], [ "P53267-1", "Aurora kinases link chromosome segregation and cell division to cancer susceptibility.", "Current opinion in genetics & development", "2004 Feb", "Meraldi P, Honda R, Nigg EA", "protein_xref_pubmed", "15108802", "protein_xref_iptmnet", "P53267" ], [ "P61830-1", "Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p.", "Cell", "2002 Oct 18", "Cheeseman IM, Anderson S, Jwa M, Green EM, Kang Js, Yates JR 3rd, Chan CS, Drubin DG, Barnes G", "protein_xref_pubmed", "12408861", "protein_xref_iptmnet", "P61830" ], [ "Q03465-1", "Ubiquitin-mediated degradation of Rpn4 is controlled by a phosphorylation-dependent ubiquitylation signal.", "Biochimica et biophysica acta", "2007-11", "Ju Donghong, Xu Haiming, Wang Xiaogang, Xie Youming", "protein_xref_pubmed", "17532487", "protein_xref_iptmnet", "Q03465" ], [ "Q03954-1", "Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p.", "Cell", "2002 Oct 18", "Cheeseman IM, Anderson S, Jwa M, Green EM, Kang Js, Yates JR 3rd, Chan CS, Drubin DG, Barnes G", "protein_xref_pubmed", "12408861", "protein_xref_iptmnet", "Q03954" ], [ "D6VTK4-1", "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "Journal of proteome research", "2007-03", "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "protein_xref_pubmed", "17330950", "protein_xref_iptmnet", "D6VTK4" ], [ "D6VTK4-1", "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "Science (New York, N.Y.)", "2009-09-25", "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "protein_xref_pubmed", "19779198", "protein_xref_iptmnet", "D6VTK4" ], [ "D6VTK4-1", "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "Genes & development", "2009-08-15", "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "protein_xref_pubmed", "19684113", "protein_xref_iptmnet", "D6VTK4" ], [ "D6VTK4-1", "Requirements for recruitment of a G protein-coupled receptor to clathrin-coated pits in budding yeast.", "Molecular biology of the cell", "2009-12", "Toshima Junko Y, Nakanishi Jun-ichi, Mizuno Kensaku, Toshima Jiro, Drubin David G", "protein_xref_pubmed", "19828733", "protein_xref_iptmnet", "D6VTK4" ], [ "D6VTK4-1", "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "Molecular & cellular proteomics : MCP", "2005-03", "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "protein_xref_pubmed", "15665377", "protein_xref_iptmnet", "D6VTK4" ], [ "D6VTK4-1", "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "Proceedings of the National Academy of Sciences of the United States of America", "2007-02-13", "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "protein_xref_pubmed", "17287358", "protein_xref_iptmnet", "D6VTK4" ], [ "D6VTK4-1", "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "Proteomics", "2009-10", "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "protein_xref_pubmed", "19795423", "protein_xref_iptmnet", "D6VTK4" ], [ "D6VTK4-1", "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "Molecular bioSystems", "2009-11", "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "protein_xref_pubmed", "19823750", "protein_xref_iptmnet", "D6VTK4" ], [ "D6VTK4-1", "Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae.", "Nature biotechnology", "2002-03", "Ficarro Scott B, McCleland Mark L, Stukenberg P Todd, Burke Daniel J, Ross Mark M, Shabanowitz Jeffrey, Hunt Donald F, White Forest M", "protein_xref_pubmed", "11875433", "protein_xref_iptmnet", "D6VTK4" ], [ "D6VTK4-1", "Regulation of the G-protein-coupled alpha-factor pheromone receptor by phosphorylation.", "Molecular and cellular biology", "1996-01", "Chen Q, Konopka J B", "protein_xref_pubmed", "8524302", "protein_xref_iptmnet", "D6VTK4" ], [ "D6W196-1", "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "Proceedings of the National Academy of Sciences of the United States of America", "2007-02-13", "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "protein_xref_pubmed", "17287358", "protein_xref_iptmnet", "D6W196" ], [ "O13297-1", "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "Molecular & cellular proteomics : MCP", "2008-07", "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "protein_xref_pubmed", "18407956", "protein_xref_iptmnet", "O13297" ], [ "O13297-1", "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "BMC genomics", "2010-12-02", "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "protein_xref_pubmed", "21126336", "protein_xref_iptmnet", "O13297" ], [ "O13297-1", "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "Science (New York, N.Y.)", "2009-09-25", "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "protein_xref_pubmed", "19779198", "protein_xref_iptmnet", "O13297" ], [ "O13297-1", "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "Proteomics", "2009-10", "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "protein_xref_pubmed", "19795423", "protein_xref_iptmnet", "O13297" ], [ "O13297-1", "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "Molecular bioSystems", "2009-11", "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "protein_xref_pubmed", "19823750", "protein_xref_iptmnet", "O13297" ], [ "O13297-1", "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "Science signaling", "2010-12-21", "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "protein_xref_pubmed", "21177495", "protein_xref_iptmnet", "O13297" ], [ "O13297-1", "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "Proceedings of the National Academy of Sciences of the United States of America", "2007-02-13", "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "protein_xref_pubmed", "17287358", "protein_xref_iptmnet", "O13297" ], [ "O13297-1", "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "Journal of proteome research", "2007-03", "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "protein_xref_pubmed", "17330950", "protein_xref_iptmnet", "O13297" ], [ "O13297-1", "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "Proceedings of the National Academy of Sciences of the United States of America", "2007-06-19", "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "protein_xref_pubmed", "17563356", "protein_xref_iptmnet", "O13297" ], [ "O13297-1", "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "Molecular biology of the cell", "2010-10-01", "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "protein_xref_pubmed", "20702584", "protein_xref_iptmnet", "O13297" ], [ "O13329-1", "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "Molecular & cellular proteomics : MCP", "2008-07", "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "protein_xref_pubmed", "18407956", "protein_xref_iptmnet", "O13329" ], [ "O13329-1", "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "Proteomics", "2009-10", "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "protein_xref_pubmed", "19795423", "protein_xref_iptmnet", "O13329" ], [ "O13329-1", "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "Molecular bioSystems", "2009-11", "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "protein_xref_pubmed", "19823750", "protein_xref_iptmnet", "O13329" ], [ "O13516-1", "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "Molecular biology of the cell", "2010-10-01", "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "protein_xref_pubmed", "20702584", "protein_xref_iptmnet", "O13516" ], [ "O13516-1", "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "BMC genomics", "2010-12-02", "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "protein_xref_pubmed", "21126336", "protein_xref_iptmnet", "O13516" ], [ "O13516-1", "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "Proceedings of the National Academy of Sciences of the United States of America", "2007-02-13", "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "protein_xref_pubmed", "17287358", "protein_xref_iptmnet", "O13516" ], [ "O13527-1", "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "Proceedings of the National Academy of Sciences of the United States of America", "2007-06-19", "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "protein_xref_pubmed", "17563356", "protein_xref_iptmnet", "O13527" ], [ "O13527-1", "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "Molecular & cellular proteomics : MCP", "2008-07", "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "protein_xref_pubmed", "18407956", "protein_xref_iptmnet", "O13527" ], [ "O13527-1", "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "Journal of proteome research", "2007-03", "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "protein_xref_pubmed", "17330950", "protein_xref_iptmnet", "O13527" ], [ "O13527-1", "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "Genes & development", "2009-08-15", "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "protein_xref_pubmed", "19684113", "protein_xref_iptmnet", "O13527" ], [ "O13527-1", "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "Science (New York, N.Y.)", "2009-09-25", "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "protein_xref_pubmed", "19779198", "protein_xref_iptmnet", "O13527" ], [ "O13527-1", "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "Science signaling", "2010-12-21", "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "protein_xref_pubmed", "21177495", "protein_xref_iptmnet", "O13527" ], [ "O13535-1", "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "Molecular & cellular proteomics : MCP", "2008-07", "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "protein_xref_pubmed", "18407956", "protein_xref_iptmnet", "O13535" ], [ "O13539-1", "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "Molecular & cellular proteomics : MCP", "2008-07", "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "protein_xref_pubmed", "18407956", "protein_xref_iptmnet", "O13539" ], [ "O13563-1", "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "Journal of proteome research", "2007-03", "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "protein_xref_pubmed", "17330950", "protein_xref_iptmnet", "O13563" ], [ "O13563-1", "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "Proceedings of the National Academy of Sciences of the United States of America", "2007-06-19", "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "protein_xref_pubmed", "17563356", "protein_xref_iptmnet", "O13563" ], [ "O13563-1", "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "Molecular & cellular proteomics : MCP", "2008-07", "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "protein_xref_pubmed", "18407956", "protein_xref_iptmnet", "O13563" ], [ "O13563-1", "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "Science (New York, N.Y.)", "2009-09-25", "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "protein_xref_pubmed", "19779198", "protein_xref_iptmnet", "O13563" ], [ "O13563-1", "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "Molecular biology of the cell", "2010-10-01", "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "protein_xref_pubmed", "20702584", "protein_xref_iptmnet", "O13563" ], [ "O13563-1", "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "BMC genomics", "2010-12-02", "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "protein_xref_pubmed", "21126336", "protein_xref_iptmnet", "O13563" ], [ "O13563-1", "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "Science signaling", "2010-12-21", "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "protein_xref_pubmed", "21177495", "protein_xref_iptmnet", "O13563" ], [ "O13563-1", "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "Genes & development", "2009-08-15", "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "protein_xref_pubmed", "19684113", "protein_xref_iptmnet", "O13563" ], [ "O13563-1", "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "Proteomics", "2009-10", "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "protein_xref_pubmed", "19795423", "protein_xref_iptmnet", "O13563" ], [ "O13563-1", "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "Molecular bioSystems", "2009-11", "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "protein_xref_pubmed", "19823750", "protein_xref_iptmnet", "O13563" ], [ "O13563-1", "Co- and post-translational modifications of the 26S proteasome in yeast.", "Proteomics", "2010-08", "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "protein_xref_pubmed", "20486117", "protein_xref_iptmnet", "O13563" ], [ "O13577-1", "Dif1 is a DNA-damage-regulated facilitator of nuclear import for ribonucleotide reductase.", "Molecular cell", "2008-10-10", "Lee Yang David, Wang Jun, Stubbe Joanne, Elledge Stephen J", "protein_xref_pubmed", "18851834", "protein_xref_iptmnet", "O13577" ] ] }, "readme": "Name\n - Yeast Proteoform Phosphorylation Citations (iPTMnet)\n\nVersion\n - v-2.3.1\n\nCreated on\n - 2022-09-02T13:26:18.780372\n\nModified on\n - 2023-09-11T20:40:34\n\nCreated by\n - [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nDescription Domain\n Keywords\n - PMID\n - journal\n - citations\n - authors\n - iPTMnet\n - PubMed\n - Phosphorylation\n\n Pipeline Steps\n - Step-1: The script parses the input file for PMIDs and accesses the NCBI Entrez infrastructure to download the publication information of the corresponding PMIDs\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-proteoform-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: yeast_proteoform_phosphorylation_sites_iptmnet.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_phosphorylation_sites_iptmnet.csv\n Output Subdomain\n Name: yeast_proteoform_citations_phosphorylation_sites_iptmnet.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_citations_phosphorylation_sites_iptmnet.csv\n Name: yeast_proteoform_citations_phosphorylation_sites_iptmnet.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_citations_phosphorylation_sites_iptmnet.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"3461\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"977\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"119\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"771\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"971\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"977\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"3461\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/yeast_proteoform_citations_phosphorylation_sites_iptmnet.csv" }