{ "bcoid": "GLY_000138", "title": "Human Proteoform Citations (UniCarbKB)", "description": "The Human Proteoform Citations (UniCarbKB) contains human [taxid:9606] publication information of glycoproteins ...", "filename": "human_proteoform_citations_glycosylation_unicarbkb.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Proteoform", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P07498-1...", "G29231AT..." ], [ "Q8WWV6-1...", "G43417UB..." ] ], "headers": [ "uniprotkb_ca...", "glytoucan_ac..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glytoucan_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" } ], [ "P07498-1", "G29231AT", "Chemical structure of neutral sugar chains isolated from human mature milk kappa-casein.", "Biochimica et biophysica acta", "1988 Feb 17", "Saito T, Itoh T, Adachi S", "protein_xref_pubmed", "3342257", "protein_xref_unicarbkb", "P07498" ], [ "Q8WWV6-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "Q8WWV6" ], [ "Q9NQ40-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "Q9NQ40" ], [ "P00747-1", "G11041DA", "Structures of the asparagine-289-linked oligosaccharides assembled on recombinant human plasminogen expressed in a Mamestra brassicae cell line (IZD-MBO503).", "Biochemistry", "1991 Jul 9", "Davidson DJ, Castellino FJ", "protein_xref_pubmed", "2065054", "protein_xref_unicarbkb", "P00747" ], [ "P07911-1", "G71906BW", "Glycosylation sites and site-specific glycosylation in human Tamm-Horsfall glycoprotein.", "Glycobiology", "1999 Jan", "van Rooijen JJ, Voskamp AF, Kamerling JP, Vliegenthart JF", "protein_xref_pubmed", "9884403", "protein_xref_unicarbkb", "P07911" ], [ "Q6UXB8-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "Q6UXB8" ], [ "P01861-1", "G68318VE", "Comparison of sialylated N-glycopeptide levels in serum of pancreatic cancer patients, acute pancreatitis patients, and healthy controls.", "Proteomics", "2014 Aug", "Kontro H, Joenvaara S, Haglund C, Renkonen R", "protein_xref_pubmed", "24841998", "protein_xref_unicarbkb", "P01861" ], [ "P25311-1", "", "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "Analytical chemistry", "2018 Jul 3", "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "protein_xref_pubmed", "29741879", "protein_xref_unicarbkb", "P25311" ], [ "P16112-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "P16112" ], [ "P02724-1", "G47180UC", "Comparative study of glycophorin A derived O-glycans from human Cad, Sd(a+) and Sd(a-) erythrocytes.", "The Biochemical journal", "1985 Dec 15", "Blanchard D, Capon C, Leroy Y, Cartron JP, Fournet B", "protein_xref_pubmed", "4091823", "protein_xref_unicarbkb", "P02724" ], [ "P04278-1", "G56682BC", "Study of the carbohydrate moiety of human serum sex hormone-binding globulin.", "Biochimica et biophysica acta", "1983 Oct 4", "Avvakumov GV, Matveentseva IV, Akhrem LV, Strel'chyonok OA, Akhrem AA", "protein_xref_pubmed", "6684483", "protein_xref_unicarbkb", "P04278" ], [ "P07911-1", "G31532GK", "Glycosylation sites and site-specific glycosylation in human Tamm-Horsfall glycoprotein.", "Glycobiology", "1999 Jan", "van Rooijen JJ, Voskamp AF, Kamerling JP, Vliegenthart JF", "protein_xref_pubmed", "9884403", "protein_xref_unicarbkb", "P07911" ], [ "P00747-1", "G56749GV", "Oligosaccharide structures present on asparagine-289 of recombinant human plasminogen expressed in a Chinese hamster ovary cell line.", "Biochemistry", "1991 Jan 22", "Davidson DJ, Castellino FJ", "protein_xref_pubmed", "1899031", "protein_xref_unicarbkb", "P00747" ], [ "P78509-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "P78509" ], [ "Q92673-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "Q92673" ], [ "P00742-1", "G43417UB", "Human urinary glycoproteomics; attachment site specific analysis of N- and O-linked glycosylations by CID and ECD.", "Molecular & cellular proteomics : MCP", "2012 Apr", "Halim A, Nilsson J, Ruetschi U, Hesse C, Larson G", "protein_xref_pubmed", "22171320", "protein_xref_unicarbkb", "P00742" ], [ "P08603-1", "G08146BT", "Site-specific N-glycan characterization of human complement factor H.", "Glycobiology", "2007 Sep", "Fenaille F, Le Mignon M, Groseil C, Ramon C, Riande S, Siret L, Bihoreau N", "protein_xref_pubmed", "17591618", "protein_xref_unicarbkb", "P08603" ], [ "P01588-1", "G17155VX", "Structures of sialylated oligosaccharides of human erythropoietin expressed in recombinant BHK-21 cells.", "European journal of biochemistry", "1993 Apr 1", "Nimtz M, Martin W, Wray V, Kloppel KD, Augustin J, Conradt HS", "protein_xref_pubmed", "8477709", "protein_xref_unicarbkb", "P01588" ], [ "P01730-1", "G45560HM", "Protein and carbohydrate structural analysis of a recombinant soluble CD4 receptor by mass spectrometry.", "The Journal of biological chemistry", "1989 Dec 15", "Carr SA, Hemling ME, Folena-Wasserman G, Sweet RW, Anumula K, Barr JR, Huddleston MJ, Taylor P", "protein_xref_pubmed", "2592374", "protein_xref_unicarbkb", "P01730" ], [ "P08861-1", "G82348BZ", "Carbohydrate structure of human pancreatic elastase 1.", "The Biochemical journal", "1991 Sep 1", "Wendorf P, Linder D, Sziegoleit A, Geyer R", "protein_xref_pubmed", "1898343", "protein_xref_unicarbkb", "P08861" ], [ "P08519-1", "G27391WQ", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "P08519" ], [ "P02724-1", "G65562ZE", "Comparative study of glycophorin A derived O-glycans from human Cad, Sd(a+) and Sd(a-) erythrocytes.", "The Biochemical journal", "1985 Dec 15", "Blanchard D, Capon C, Leroy Y, Cartron JP, Fournet B", "protein_xref_pubmed", "4091823", "protein_xref_unicarbkb", "P02724" ], [ "P01588-1", "G68892PJ", "Comparative structural study of N-linked oligosaccharides of urinary and recombinant erythropoietins.", "Biochemistry", "1988 Jul 26", "Tsuda E, Goto M, Murakami A, Akai K, Ueda M, Kawanishi G, Takahashi N, Sasaki R, Chiba H, Ishihara H, et al.", "protein_xref_pubmed", "3179269", "protein_xref_unicarbkb", "P01588" ], [ "P01588-1", "G30460NZ", "Structural analysis of sulfated N-linked oligosaccharides in erythropoietin.", "Glycobiology", "2001 Dec", "Kawasaki N, Haishima Y, Ohta M, Itoh S, Hyuga M, Hyuga S, Hayakawa T", "protein_xref_pubmed", "11805077", "protein_xref_unicarbkb", "P01588" ], [ "Q05707-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "Q05707" ], [ "Q4LDE5-1", "G43417UB", "Human urinary glycoproteomics; attachment site specific analysis of N- and O-linked glycosylations by CID and ECD.", "Molecular & cellular proteomics : MCP", "2012 Apr", "Halim A, Nilsson J, Ruetschi U, Hesse C, Larson G", "protein_xref_pubmed", "22171320", "protein_xref_unicarbkb", "Q4LDE5" ], [ "P07911-1", "G90987JA", "Glycosylation sites and site-specific glycosylation in human Tamm-Horsfall glycoprotein.", "Glycobiology", "1999 Jan", "van Rooijen JJ, Voskamp AF, Kamerling JP, Vliegenthart JF", "protein_xref_pubmed", "9884403", "protein_xref_unicarbkb", "P07911" ], [ "P08709-1", "G50739NP", "Mass spectrometric characterization of N- and O-glycans of plasma-derived coagulation factor VII.", "Glycoconjugate journal", "2008 Dec", "Fenaille F, Groseil C, Ramon C, Riande S, Siret L, Chtourou S, Bihoreau N", "protein_xref_pubmed", "18642129", "protein_xref_unicarbkb", "P08709" ], [ "P01730-1", "G78059CC", "Protein and carbohydrate structural analysis of a recombinant soluble CD4 receptor by mass spectrometry.", "The Journal of biological chemistry", "1989 Dec 15", "Carr SA, Hemling ME, Folena-Wasserman G, Sweet RW, Anumula K, Barr JR, Huddleston MJ, Taylor P", "protein_xref_pubmed", "2592374", "protein_xref_unicarbkb", "P01730" ], [ "P00734-1", "G91365ZQ", "Studies on the structures of the carbohydrate moiety of human prothrombin.", "Journal of biochemistry", "1981 Oct", "Mizuochi T, Fujii J, Kisiel W, Kobata A", "protein_xref_pubmed", "7309709", "protein_xref_unicarbkb", "P00734" ], [ "P01215-1", "G24413UY", "Carbohydrate and peptide structure of the alpha- and beta-subunits of human chorionic gonadotropin from normal and aberrant pregnancy and choriocarcinoma.", "Endocrine", "1997 Aug", "Elliott MM, Kardana A, Lustbader JW, Cole LA", "protein_xref_pubmed", "9449027", "protein_xref_unicarbkb", "P01215" ], [ "P16150-1", "G65562ZE", "Structural variations of O-linked oligosaccharides present in leukosialin isolated from erythroid, myeloid, and T-lymphoid cell lines.", "The Journal of biological chemistry", "1986 Sep 25", "Carlsson SR, Sasaki H, Fukuda M", "protein_xref_pubmed", "2943741", "protein_xref_unicarbkb", "P16150" ], [ "P02771-1", "G66937TJ", "Unique structure of glycopeptide from alpha-fetoprotein produced in human hepatoma cell line, as determined by 1H-nuclear magnetic resonance spectroscopy.", "Clinical chemistry", "1990 Jun", "Terrana B, Tecce MF, Manetti R, Ceccarini C, Lamba D, Segre AL", "protein_xref_pubmed", "1694115", "protein_xref_unicarbkb", "P02771" ], [ "Q14766-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "Q14766" ], [ "P01588-1", "G47279LF", "Structures of mucin-type sugar chains on human erythropoietins purified from urine and the culture medium of recombinant Chinese hamster ovary cells.", "Archives of biochemistry and biophysics", "1993 Mar", "Inoue N, Takeuchi M, Asano K, Shimizu R, Takasaki S, Kobata A", "protein_xref_pubmed", "8460945", "protein_xref_unicarbkb", "P01588" ], [ "P01215-1", "G25835MT", "Site-specific N-glycosylation of human chorionic gonadotrophin--structural analysis of glycopeptides by one- and two-dimensional 1H NMR spectroscopy.", "Glycobiology", "1991 Sep", "Weisshaar G, Hiyama J, Renwick AG", "protein_xref_pubmed", "1820200", "protein_xref_unicarbkb", "P01215" ], [ "P08709-1", "G71527NE", "Mass spectrometric characterization of N- and O-glycans of plasma-derived coagulation factor VII.", "Glycoconjugate journal", "2008 Dec", "Fenaille F, Groseil C, Ramon C, Riande S, Siret L, Chtourou S, Bihoreau N", "protein_xref_pubmed", "18642129", "protein_xref_unicarbkb", "P08709" ], [ "Q14624-1", "", "Site-specific glycan microheterogeneity of inter-alpha-trypsin inhibitor heavy chain H4.", "Journal of proteome research", "2014 Jul 3", "Chandler KB, Brnakova Z, Sanda M, Wang S, Stalnaker SH, Bridger R, Zhao P, Wells L, Edwards NJ, Goldman R", "protein_xref_pubmed", "24884609", "protein_xref_unicarbkb", "Q14624" ], [ "P02724-1", "G33350UC", "Structures of the asparagine-linked sugar chains of glycophorin A.", "The Journal of biological chemistry", "1980 Oct 25", "Yoshima H, Furthmayr H, Kobata A", "protein_xref_pubmed", "7430095", "protein_xref_unicarbkb", "P02724" ], [ "P04275-1", "G16175ZV", "Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical N-Glycosylation Sites on Albumin and alpha-1B-Glycoprotein.", "Analytical chemistry", "2018 May 15", "Sun S, Hu Y, Jia L, Eshghi ST, Liu Y, Shah P, Zhang H", "protein_xref_pubmed", "29671580", "protein_xref_unicarbkb", "P04275" ], [ "P02786-1", "G74910CR", "Human transferrin receptor contains O-linked oligosaccharides.", "The Journal of biological chemistry", "1990 Jan 5", "Do SI, Enns C, Cummings RD", "protein_xref_pubmed", "2403553", "protein_xref_unicarbkb", "P02786" ], [ "O94905-1", "G01650EU", "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "Analytical chemistry", "2018 Jul 3", "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "protein_xref_pubmed", "29741879", "protein_xref_unicarbkb", "O94905" ], [ "Q9UFP1-1", "G43417UB", "Human urinary glycoproteomics; attachment site specific analysis of N- and O-linked glycosylations by CID and ECD.", "Molecular & cellular proteomics : MCP", "2012 Apr", "Halim A, Nilsson J, Ruetschi U, Hesse C, Larson G", "protein_xref_pubmed", "22171320", "protein_xref_unicarbkb", "Q9UFP1" ], [ "P07911-1", "G99808VS", "Pregnancy-associated changes in oligomannose oligosaccharides of human and bovine uromodulin (Tamm-Horsfall glycoprotein).", "Glycoconjugate journal", "1990", "Smagula RM, Van Halbeek H, Decker JM, Muchmore AV, Moody CE, Sherblom AP", "protein_xref_pubmed", "2136357", "protein_xref_unicarbkb", "P07911" ], [ "P01876-1", "G88374WZ", "Comparison of sialylated N-glycopeptide levels in serum of pancreatic cancer patients, acute pancreatitis patients, and healthy controls.", "Proteomics", "2014 Aug", "Kontro H, Joenvaara S, Haglund C, Renkonen R", "protein_xref_pubmed", "24841998", "protein_xref_unicarbkb", "P01876" ], [ "P11279-1", "G58001LT", "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "Analytical chemistry", "2018 Jul 3", "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "protein_xref_pubmed", "29741879", "protein_xref_unicarbkb", "P11279" ], [ "P08603-1", "G94917XT", "Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical N-Glycosylation Sites on Albumin and alpha-1B-Glycoprotein.", "Analytical chemistry", "2018 May 15", "Sun S, Hu Y, Jia L, Eshghi ST, Liu Y, Shah P, Zhang H", "protein_xref_pubmed", "29671580", "protein_xref_unicarbkb", "P08603" ], [ "P11279-1", "G94917XT", "Glycoproteomic analysis of the secretome of human endothelial cells.", "Molecular & cellular proteomics : MCP", "2013 Apr", "Yin X, Bern M, Xing Q, Ho J, Viner R, Mayr M", "protein_xref_pubmed", "23345538", "protein_xref_unicarbkb", "P11279" ], [ "Q5H9R7-1", "G60033FS", "Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical N-Glycosylation Sites on Albumin and alpha-1B-Glycoprotein.", "Analytical chemistry", "2018 May 15", "Sun S, Hu Y, Jia L, Eshghi ST, Liu Y, Shah P, Zhang H", "protein_xref_pubmed", "29671580", "protein_xref_unicarbkb", "Q5H9R7" ], [ "P02679-1", "G91365ZQ", "Carbohydrate structure of human fibrinogen. Use of 300-MHz 1H-NMR to characterize glycosidase-treated glycopeptides.", "The Journal of biological chemistry", "1982 Aug 25", "Townsend RR, Hilliker E, Li YT, Laine RA, Bell WR, Lee YC", "protein_xref_pubmed", "7107587", "protein_xref_unicarbkb", "P02679" ], [ "P01730-1", "G03860PZ", "Protein and carbohydrate structural analysis of a recombinant soluble CD4 receptor by mass spectrometry.", "The Journal of biological chemistry", "1989 Dec 15", "Carr SA, Hemling ME, Folena-Wasserman G, Sweet RW, Anumula K, Barr JR, Huddleston MJ, Taylor P", "protein_xref_pubmed", "2592374", "protein_xref_unicarbkb", "P01730" ], [ "P07911-1", "G96921ZU", "Pregnancy-associated changes in oligomannose oligosaccharides of human and bovine uromodulin (Tamm-Horsfall glycoprotein).", "Glycoconjugate journal", "1990", "Smagula RM, Van Halbeek H, Decker JM, Muchmore AV, Moody CE, Sherblom AP", "protein_xref_pubmed", "2136357", "protein_xref_unicarbkb", "P07911" ], [ "P04114-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "P04114" ], [ "P16150-1", "G00031MO", "Altered O-glycan synthesis in lymphocytes from patients with Wiskott-Aldrich syndrome.", "The Journal of experimental medicine", "1991 Jun 1", "Piller F, Le Deist F, Weinberg KI, Parkman R, Fukuda M", "protein_xref_pubmed", "2033371", "protein_xref_unicarbkb", "P16150" ], [ "Q92876-1", "G44369QM", "Differential N-glycosylation of kallikrein 6 derived from ovarian cancer cells or the central nervous system.", "Molecular & cellular proteomics : MCP", "2009 Apr", "Kuzmanov U, Jiang N, Smith CR, Soosaipillai A, Diamandis EP", "protein_xref_pubmed", "19088065", "protein_xref_unicarbkb", "Q92876" ], [ "Q9ULI3-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "Q9ULI3" ], [ "P03952-1", "G42358LZ", "Computational framework for identification of intact glycopeptides in complex samples.", "Analytical chemistry", "2014 Jan 7", "Mayampurath A, Yu CY, Song E, Balan J, Mechref Y, Tang H", "protein_xref_pubmed", "24279413", "protein_xref_unicarbkb", "P03952" ], [ "P07911-1", "G32659RY", "Glycosylation sites and site-specific glycosylation in human Tamm-Horsfall glycoprotein.", "Glycobiology", "1999 Jan", "van Rooijen JJ, Voskamp AF, Kamerling JP, Vliegenthart JF", "protein_xref_pubmed", "9884403", "protein_xref_unicarbkb", "P07911" ], [ "P25311-1", "G08293MJ", "Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical N-Glycosylation Sites on Albumin and alpha-1B-Glycoprotein.", "Analytical chemistry", "2018 May 15", "Sun S, Hu Y, Jia L, Eshghi ST, Liu Y, Shah P, Zhang H", "protein_xref_pubmed", "29671580", "protein_xref_unicarbkb", "P25311" ], [ "Q9Y5L3-1", "", "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "Analytical chemistry", "2018 Jul 3", "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "protein_xref_pubmed", "29741879", "protein_xref_unicarbkb", "Q9Y5L3" ], [ "P07498-1", "G69500TM", "Chemical structure of neutral sugar chains isolated from human mature milk kappa-casein.", "Biochimica et biophysica acta", "1988 Feb 17", "Saito T, Itoh T, Adachi S", "protein_xref_pubmed", "3342257", "protein_xref_unicarbkb", "P07498" ], [ "P01215-1", "G14358WN", "The asparagine-linked oligosaccharides at individual glycosylation sites in human thyrotrophin.", "Glycobiology", "1992 Oct", "Hiyama J, Weisshaar G, Renwick AG", "protein_xref_pubmed", "1457969", "protein_xref_unicarbkb", "P01215" ], [ "P07288-1", "", "Glycoproteomics: identifying the glycosylation of prostate specific antigen at normal and high isoelectric points by LC-MS/MS.", "Journal of proteome research", "2014 Dec 5", "Song E, Mayampurath A, Yu CY, Tang H, Mechref Y", "protein_xref_pubmed", "25327667", "protein_xref_unicarbkb", "P07288" ], [ "P01215-1", "G78890OB", "Carbohydrate and peptide structure of the alpha- and beta-subunits of human chorionic gonadotropin from normal and aberrant pregnancy and choriocarcinoma.", "Endocrine", "1997 Aug", "Elliott MM, Kardana A, Lustbader JW, Cole LA", "protein_xref_pubmed", "9449027", "protein_xref_unicarbkb", "P01215" ], [ "P04114-1", "G88374WZ", "Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical N-Glycosylation Sites on Albumin and alpha-1B-Glycoprotein.", "Analytical chemistry", "2018 May 15", "Sun S, Hu Y, Jia L, Eshghi ST, Liu Y, Shah P, Zhang H", "protein_xref_pubmed", "29671580", "protein_xref_unicarbkb", "P04114" ], [ "P02771-1", "G36191CD", "Carbohydrate structures of human alpha-fetoprotein of patients with hepatocellular carcinoma: presence of fucosylated and non-fucosylated triantennary glycans.", "British journal of cancer", "1993 Mar", "Aoyagi Y, Suzuki Y, Igarashi K, Saitoh A, Oguro M, Yokota T, Mori S, Suda T, Isemura M, Asakura H", "protein_xref_pubmed", "7679920", "protein_xref_unicarbkb", "P02771" ], [ "P02724-1", "G33350UC", "Comparative study of glycophorin A derived O-glycans from human Cad, Sd(a+) and Sd(a-) erythrocytes.", "The Biochemical journal", "1985 Dec 15", "Blanchard D, Capon C, Leroy Y, Cartron JP, Fournet B", "protein_xref_pubmed", "4091823", "protein_xref_unicarbkb", "P02724" ], [ "P39060-3", "G29068FM", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "P39060" ], [ "P28300-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "P28300" ], [ "O00220-1", "G43417UB", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "O00220" ], [ "P07498-1", "G41424HD", "Chemical structure of neutral sugar chains isolated from human mature milk kappa-casein.", "Biochimica et biophysica acta", "1988 Feb 17", "Saito T, Itoh T, Adachi S", "protein_xref_pubmed", "3342257", "protein_xref_unicarbkb", "P07498" ], [ "P36955-1", "G29068FM", "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "Molecular systems biology", "2018 Nov 20", "Yang W, Ao M, Hu Y, Li QK, Zhang H", "protein_xref_pubmed", "30459171", "protein_xref_unicarbkb", "P36955" ], [ "P10646-1", "G45359RY", "The asparagine-linked oligosaccharides on tissue factor pathway inhibitor terminate with SO4-4GalNAc beta 1, 4GlcNAc beta 1,2 Mana alpha.", "The Journal of biological chemistry", "1992 Sep 25", "Smith PL, Skelton TP, Fiete D, Dharmesh SM, Beranek MC, MacPhail L, Broze GJ Jr, Baenziger JU", "protein_xref_pubmed", "1388166", "protein_xref_unicarbkb", "P10646" ], [ "P00750-1", "G40702WU", "The glycosylation of Bowes melanoma tissue plasminogen activator: lectin mapping, reaction with anti-L2/HNK-1 antibodies and the presence of sulphated/glucuronic acid containing glycans.", "The Biochemical journal", "1996 Jun 1", "Jaques AJ, Opdenakker G, Rademacher TW, Dwek RA, Zamze SE", "protein_xref_pubmed", "8687384", "protein_xref_unicarbkb", "P00750" ], [ "P02771-1", "G78059CC", "Sugar chain of alpha-fetoprotein produced in human yolk sac tumor.", "Cancer research", "1983 Oct", "Yamashita K, Hitoi A, Tsuchida Y, Nishi S, Kobata A", "protein_xref_pubmed", "6192908", "protein_xref_unicarbkb", "P02771" ], [ "P01588-1", "G50489VC", "Recombinant human erythropoietin produced by Namalwa cells.", "DNA (Mary Ann Liebert, Inc.)", "1989 Jul-Aug", "Yanagi H, Yoshima T, Ogawa I, Okamoto M", "protein_xref_pubmed", "2550193", "protein_xref_unicarbkb", "P01588" ], [ "P02724-1", "G16370GQ", "Comparative study of glycophorin A derived O-glycans from human Cad, Sd(a+) and Sd(a-) erythrocytes.", "The Biochemical journal", "1985 Dec 15", "Blanchard D, Capon C, Leroy Y, Cartron JP, Fournet B", "protein_xref_pubmed", "4091823", "protein_xref_unicarbkb", "P02724" ], [ "P07911-1", "G32659RY", "Pregnancy-associated changes in oligomannose oligosaccharides of human and bovine uromodulin (Tamm-Horsfall glycoprotein).", "Glycoconjugate journal", "1990", "Smagula RM, Van Halbeek H, Decker JM, Muchmore AV, Moody CE, Sherblom AP", "protein_xref_pubmed", "2136357", "protein_xref_unicarbkb", "P07911" ], [ "P05156-1", "G94917XT", "Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical N-Glycosylation Sites on Albumin and alpha-1B-Glycoprotein.", "Analytical chemistry", "2018 May 15", "Sun S, Hu Y, Jia L, Eshghi ST, Liu Y, Shah P, Zhang H", "protein_xref_pubmed", "29671580", "protein_xref_unicarbkb", "P05156" ], [ "P41222-1", "", "Carbohydrate structures of beta-trace protein from human cerebrospinal fluid: evidence for `brain-type` N-glycosylation.", "Journal of neurochemistry", "1994 Dec", "Hoffmann A, Nimtz M, Wurster U, Conradt HS", "protein_xref_pubmed", "7525874", "protein_xref_unicarbkb", "P41222" ], [ "P14625-1", "", "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "Analytical chemistry", "2018 Jul 3", "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "protein_xref_pubmed", "29741879", "protein_xref_unicarbkb", "P14625" ], [ "P12110-1", "", "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "Analytical chemistry", "2018 Jul 3", "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "protein_xref_pubmed", "29741879", "protein_xref_unicarbkb", "P12110" ], [ "P01588-1", "G56682BC", "Structures of mucin-type sugar chains on human erythropoietins purified from urine and the culture medium of recombinant Chinese hamster ovary cells.", "Archives of biochemistry and biophysics", "1993 Mar", "Inoue N, Takeuchi M, Asano K, Shimizu R, Takasaki S, Kobata A", "protein_xref_pubmed", "8460945", "protein_xref_unicarbkb", "P01588" ], [ "P01588-1", "G16873YG", "Structures of sialylated oligosaccharides of human erythropoietin expressed in recombinant BHK-21 cells.", "European journal of biochemistry", "1993 Apr 1", "Nimtz M, Martin W, Wray V, Kloppel KD, Augustin J, Conradt HS", "protein_xref_pubmed", "8477709", "protein_xref_unicarbkb", "P01588" ] ] }, "readme": "Name\n - Human Proteoform Citations (UniCarbKB)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-04-16T16:31:37.511217\n\nModified on\n - 2022-01-19T11:22:32.816914\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.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 - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Human Proteoform Citations (UniCarbKB) contains human [taxid:9606] publication information of glycoproteins from UniCarbKB. The script accesses the NCBI ENTREZ infrastructure to retrieve the publication information of the given PMID from UniCarbKB. The dataset is contributed by UniCarbKB and processed by GlyGen. If you use this dataset please provide proper attribution to UniCarbKB and GlyGen [UniCarbKB - https://academic.oup.com/nar/article/42/D1/D215/1052197 ,https://doi.org/10.1093/nar/gkt1128]. \n\nDescription Domain\n Keywords\n - PMID\n - journal\n - citations\n - authors\n - UniCarbKB\n - PubMed\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/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: human_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_proteoform_glycosylation_sites_unicarbkb.csv\n Output Subdomain\n Name: human_proteoform_citations_glycosylation_unicarbkb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_proteoform_citations_glycosylation_unicarbkb.csv\n Name: human_proteoform_citations_glycosylation_unicarbkb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_proteoform_citations_glycosylation_unicarbkb.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_glycosylation_unicarbkb.csv" }