{ "bcoid": "GLY_000567", "title": "Human Proteoform Phosphorylation Citations (iPTMnet)", "description": "", "filename": "human_proteoform_citations_phosphorylation_iptmnet.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Proteoform", "tags": "Phosphorylation Citations (iPTMnet)", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q9NYM9-1...", "TiO(2)-based..." ], [ "Q9NYM9-1...", "A quantitati..." ] ], "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" } ], [ "Q9NYM9-1", "TiO(2)-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment.", "Journal of proteome research", "2008 Aug", "Thingholm TE, Larsen MR, Ingrell CR, Kassem M, Jensen ON", "protein_xref_pubmed", "18578522", "protein_xref_iptmnet", "A0A0C4DH16" ], [ "Q9NYM9-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A0A0C4DH16" ], [ "Q9NYM9-1", "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "Analytical chemistry", "2009 Jun 1", "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "protein_xref_pubmed", "19413330", "protein_xref_iptmnet", "A0A0C4DH16" ], [ "Q9NYM9-1", "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "Molecular & cellular proteomics : MCP", "2009 Dec", "Pan C, Olsen JV, Daub H, Mann M", "protein_xref_pubmed", "19651622", "protein_xref_iptmnet", "A0A0C4DH16" ], [ "Q9NYM9-1", "Phosphoproteomic analysis of human embryonic stem cells.", "Cell stem cell", "2009 Aug 7", "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "protein_xref_pubmed", "19664994", "protein_xref_iptmnet", "A0A0C4DH16" ], [ "Q9NYM9-1", "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "Cell stem cell", "2009 Aug 7", "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "protein_xref_pubmed", "19664995", "protein_xref_iptmnet", "A0A0C4DH16" ], [ "Q9NYM9-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A0A0C4DH16" ], [ "A0A140G945-1", "Shotgun identification of protein modifications from protein complexes and lens tissue.", "Proceedings of the National Academy of Sciences of the United States of America", "2002 Jun 11", "MacCoss MJ, McDonald WH, Saraf A, Sadygov R, Clark JM, Tasto JJ, Gould KL, Wolters D, Washburn M, Weiss A, Clark JI, Yates JR 3rd", "protein_xref_pubmed", "12060738", "protein_xref_iptmnet", "A0A140G945-1" ], [ "Q13555-1", "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "Molecular cell", "2008 Aug 8", "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "protein_xref_pubmed", "18691976", "protein_xref_iptmnet", "A0A2Q3DQE3" ], [ "Q13555-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A0A2Q3DQE3" ], [ "Q13555-1", "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "Cell", "2006 Nov 3", "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "protein_xref_pubmed", "17081983", "protein_xref_iptmnet", "A0A2Q3DQE3" ], [ "Q13555-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A0A2Q3DQE3" ], [ "Q13555-1", "Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer.", "Analytical chemistry", "2010 Feb 1", "Raijmakers R, Kraiczek K, de Jong AP, Mohammed S, Heck AJ", "protein_xref_pubmed", "20058876", "protein_xref_iptmnet", "A0A2Q3DQE3" ], [ "A0AV96-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A0AV96-1" ], [ "A0AVF1-1", "Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.", "Proteomics", "2008 May", "Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X", "protein_xref_pubmed", "18491316", "protein_xref_iptmnet", "A0AVF1-1" ], [ "A0AVT1-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A0AVT1-1" ], [ "A0FGR8-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A0FGR8" ], [ "A0FGR8-1", "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "Journal of proteome research", "2008 Oct", "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "protein_xref_pubmed", "18767875", "protein_xref_iptmnet", "A0FGR8" ], [ "A0FGR8-1", "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "Molecular & cellular proteomics : MCP", "2009 Dec", "Pan C, Olsen JV, Daub H, Mann M", "protein_xref_pubmed", "19651622", "protein_xref_iptmnet", "A0FGR8" ], [ "A0FGR9-1", "Motif-specific sampling of phosphoproteomes.", "Journal of proteome research", "2008 May", "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "protein_xref_pubmed", "18452278", "protein_xref_iptmnet", "A0FGR9-1" ], [ "A0JNW5-1", "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "Cell", "2006 Nov 3", "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "protein_xref_pubmed", "17081983", "protein_xref_iptmnet", "A0JNW5-1" ], [ "A0JNW5-1", "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "Analytical chemistry", "2009 Jun 1", "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "protein_xref_pubmed", "19413330", "protein_xref_iptmnet", "A0JNW5-1" ], [ "A0JNW5-1", "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "Molecular & cellular proteomics : MCP", "2009 Dec", "Pan C, Olsen JV, Daub H, Mann M", "protein_xref_pubmed", "19651622", "protein_xref_iptmnet", "A0JNW5-1" ], [ "A0JNW5-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A0JNW5-1" ], [ "A1KXE4-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A1KXE4-1" ], [ "A1L020-1", "Phosphoproteomic analysis of human embryonic stem cells.", "Cell stem cell", "2009 Aug 7", "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "protein_xref_pubmed", "19664994", "protein_xref_iptmnet", "A1L020" ], [ "A1L170-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A1L170-1" ], [ "A1L170-1", "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "Molecular cell", "2008 Aug 8", "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "protein_xref_pubmed", "18691976", "protein_xref_iptmnet", "A1L170-1" ], [ "A1L170-1", "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "Analytical chemistry", "2009 Jun 1", "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "protein_xref_pubmed", "19413330", "protein_xref_iptmnet", "A1L170-1" ], [ "A1L170-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A1L170-1" ], [ "A1L170-1", "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "Electrophoresis", "2010 Mar", "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "protein_xref_pubmed", "20166139", "protein_xref_iptmnet", "A1L170-1" ], [ "A1L170-1", "Phosphoproteomic analysis of human embryonic stem cells.", "Cell stem cell", "2009 Aug 7", "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "protein_xref_pubmed", "19664994", "protein_xref_iptmnet", "A1L170-1" ], [ "A1L170-1", "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "Cell stem cell", "2009 Aug 7", "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "protein_xref_pubmed", "19664995", "protein_xref_iptmnet", "A1L170-1" ], [ "A1X283-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A1X283" ], [ "A1X283-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A1X283" ], [ "A1X283-1", "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "Molecular & cellular proteomics : MCP", "2009 Dec", "Pan C, Olsen JV, Daub H, Mann M", "protein_xref_pubmed", "19651622", "protein_xref_iptmnet", "A1X283" ], [ "A1X283-1", "Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer.", "Cell", "2007 Dec 14", "Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ", "protein_xref_pubmed", "18083107", "protein_xref_iptmnet", "A1X283" ], [ "A1X283-1", "TiO(2)-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment.", "Journal of proteome research", "2008 Aug", "Thingholm TE, Larsen MR, Ingrell CR, Kassem M, Jensen ON", "protein_xref_pubmed", "18578522", "protein_xref_iptmnet", "A1X283" ], [ "A2A2Y4-1", "Motif-specific sampling of phosphoproteomes.", "Journal of proteome research", "2008 May", "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "protein_xref_pubmed", "18452278", "protein_xref_iptmnet", "A2A2Y4-1" ], [ "A2RRP1-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A2RRP1-1" ], [ "A2RRP1-1", "Motif-specific sampling of phosphoproteomes.", "Journal of proteome research", "2008 May", "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "protein_xref_pubmed", "18452278", "protein_xref_iptmnet", "A2RRP1-1" ], [ "A2RRP1-1", "Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.", "Proteomics", "2008 May", "Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X", "protein_xref_pubmed", "18491316", "protein_xref_iptmnet", "A2RRP1-1" ], [ "A2RRP1-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A2RRP1-1" ], [ "A2RRP1-1", "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "Molecular & cellular proteomics : MCP", "2009 Dec", "Pan C, Olsen JV, Daub H, Mann M", "protein_xref_pubmed", "19651622", "protein_xref_iptmnet", "A2RRP1-1" ], [ "A2RRP1-1", "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "Electrophoresis", "2010 Mar", "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "protein_xref_pubmed", "20166139", "protein_xref_iptmnet", "A2RRP1-1" ], [ "A2RU67-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A2RU67" ], [ "A2RU67-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A2RU67" ], [ "A2RU67-1", "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "Analytical chemistry", "2009 Jun 1", "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "protein_xref_pubmed", "19413330", "protein_xref_iptmnet", "A2RU67" ], [ "A2RUS2-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A2RUS2" ], [ "A2VDJ0-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A2VDJ0-1" ], [ "A4D1E1-1", "Phosphoproteomic analysis of primary human multiple myeloma cells.", "Journal of proteomics", "2010 May 7", "Ge F, Xiao CL, Yin XF, Lu CH, Zeng HL, He QY", "protein_xref_pubmed", "20230923", "protein_xref_iptmnet", "A4D1E1" ], [ "A4D1E1-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A4D1E1" ], [ "A4D1E9-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A4D1E9-1" ], [ "A4D1P6-1", "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "Nature biotechnology", "2006 Oct", "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "protein_xref_pubmed", "16964243", "protein_xref_iptmnet", "A4D1P6-1" ], [ "A4D1P6-1", "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "Molecular & cellular proteomics : MCP", "2009 Dec", "Pan C, Olsen JV, Daub H, Mann M", "protein_xref_pubmed", "19651622", "protein_xref_iptmnet", "A4D1P6-1" ], [ "A4D1S0-1", "Phosphoproteomic analysis of human embryonic stem cells.", "Cell stem cell", "2009 Aug 7", "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "protein_xref_pubmed", "19664994", "protein_xref_iptmnet", "A4D1S0-1" ], [ "A4D1S0-1", "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "Analytical chemistry", "2009 Jun 1", "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "protein_xref_pubmed", "19413330", "protein_xref_iptmnet", "A4D1S0-1" ], [ "A4D1S0-1", "Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.", "Proteomics", "2008 May", "Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X", "protein_xref_pubmed", "18491316", "protein_xref_iptmnet", "A4D1S0-1" ], [ "A4D2B0-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A4D2B0" ], [ "A4D2H0-1", "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "Cell", "2006 Nov 3", "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "protein_xref_pubmed", "17081983", "protein_xref_iptmnet", "A4D2H0" ], [ "A4D2H0-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A4D2H0" ], [ "A4FU69-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A4FU69" ], [ "A5D8V6-1", "Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.", "Proteomics", "2008 May", "Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X", "protein_xref_pubmed", "18491316", "protein_xref_iptmnet", "A5D8V6" ], [ "A5PKW4-1", "Phosphoproteomic analysis of the developing mouse brain.", "Molecular & cellular proteomics : MCP", "2004 Nov", "Ballif BA, Villen J, Beausoleil SA, Schwartz D, Gygi SP", "protein_xref_pubmed", "15345747", "protein_xref_iptmnet", "A5PKW4-1" ], [ "A5PKW4-1", "Motif-specific sampling of phosphoproteomes.", "Journal of proteome research", "2008 May", "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "protein_xref_pubmed", "18452278", "protein_xref_iptmnet", "A5PKW4-1" ], [ "A5PL33-1", "Phosphoproteomic analysis of human embryonic stem cells.", "Cell stem cell", "2009 Aug 7", "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "protein_xref_pubmed", "19664994", "protein_xref_iptmnet", "A5PL33-1" ], [ "A5YKK6-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A5YKK6-1" ], [ "A5YKK6-1", "Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction.", "Molecular & cellular proteomics : MCP", "2007 Nov", "Tang LY, Deng N, Wang LS, Dai J, Wang ZL, Jiang XS, Li SJ, Li L, Sheng QH, Wu DQ, Li L, Zeng R", "protein_xref_pubmed", "17693683", "protein_xref_iptmnet", "A5YKK6-1" ], [ "A6H8Y1-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A6H8Y1-1" ], [ "A6H8Y1-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A6H8Y1-1" ], [ "A6H8Y1-1", "ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.", "Science (New York, N.Y.)", "2007 May 25", "Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ", "protein_xref_pubmed", "17525332", "protein_xref_iptmnet", "A6H8Y1-1" ], [ "A6NC98-1", "Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer.", "Analytical chemistry", "2010 Feb 1", "Raijmakers R, Kraiczek K, de Jong AP, Mohammed S, Heck AJ", "protein_xref_pubmed", "20058876", "protein_xref_iptmnet", "A6NC98-1" ], [ "A6ND36-1", "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "Cell stem cell", "2009 Aug 7", "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "protein_xref_pubmed", "19664995", "protein_xref_iptmnet", "A6ND36-1" ], [ "A6ND36-1", "A quantitative atlas of mitotic phosphorylation.", "Proceedings of the National Academy of Sciences of the United States of America", "2008 Aug 5", "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "protein_xref_pubmed", "18669648", "protein_xref_iptmnet", "A6ND36-1" ], [ "A6ND36-1", "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "Electrophoresis", "2010 Mar", "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "protein_xref_pubmed", "20166139", "protein_xref_iptmnet", "A6ND36-1" ], [ "A6ND36-1", "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "Nature biotechnology", "2006 Oct", "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "protein_xref_pubmed", "16964243", "protein_xref_iptmnet", "A6ND36-1" ], [ "A6NDG6-1", "Motif-specific sampling of phosphoproteomes.", "Journal of proteome research", "2008 May", "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "protein_xref_pubmed", "18452278", "protein_xref_iptmnet", "A6NDG6" ], [ "A6NEK1-1", "Motif-specific sampling of phosphoproteomes.", "Journal of proteome research", "2008 May", "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "protein_xref_pubmed", "18452278", "protein_xref_iptmnet", "A6NEK1" ], [ "A6NEL2-1", "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "Molecular & cellular proteomics : MCP", "2009 Dec", "Pan C, Olsen JV, Daub H, Mann M", "protein_xref_pubmed", "19651622", "protein_xref_iptmnet", "A6NEL2" ], [ "A6NEQ2-1", "Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction.", "Molecular & cellular proteomics : MCP", "2007 Nov", "Tang LY, Deng N, Wang LS, Dai J, Wang ZL, Jiang XS, Li SJ, Li L, Sheng QH, Wu DQ, Li L, Zeng R", "protein_xref_pubmed", "17693683", "protein_xref_iptmnet", "A6NEQ2" ], [ "A6NGG8-1", "Multiple myeloma phosphotyrosine proteomic profile associated with FGFR3 expression, ligand activation, and drug inhibition.", "Proceedings of the National Academy of Sciences of the United States of America", "2009 Nov 24", "St-Germain JR, Taylor P, Tong J, Jin LL, Nikolic A, Stewart II, Ewing RM, Dharsee M, Li Z, Trudel S, Moran MF", "protein_xref_pubmed", "19901323", "protein_xref_iptmnet", "A6NGG8" ], [ "A6NHL2-1", "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "Science signaling", "2010 Jan 12", "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "protein_xref_pubmed", "20068231", "protein_xref_iptmnet", "A6NHL2-1" ], [ "A6NHL2-1", "Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra.", "Journal of proteome research", "2007 Nov", "Yu LR, Zhu Z, Chan KC, Issaq HJ, Dimitrov DS, Veenstra TD", "protein_xref_pubmed", "17924679", "protein_xref_iptmnet", "A6NHL2-1" ], [ "A6NHN0-1", "Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.", "Proteomics", "2008 May", "Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X", "protein_xref_pubmed", "18491316", "protein_xref_iptmnet", "A6NHN0" ] ] }, "readme": "Name\n - Human Proteoform Phosphorylation Citations (iPTMnet)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2021-06-03T17:29:17.656153\n\nModified on\n - 2021-10-15T16:18:35.745590\n\nCreated by\n - [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nExecution Domain\n Scripts\n\n Software Prerequisites\n\nI/O Domain\n Output Subdomain\n Name: human_proteoform_citations_phosphorylation_iptmnet.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/human_proteoform_citations_phosphorylation_iptmnet.csv\n Name: human_proteoform_citations_phosphorylation_iptmnet.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/human_proteoform_citations_phosphorylation_iptmnet.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"3\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/human_proteoform_citations_phosphorylation_iptmnet.csv" }