{ "bcoid": "GLY_000516", "title": "Human Proteoform Citations (Literature Mining)", "description": "The dataset provides citation details corresponding to the PubMed ID (PMID) from file https://data.glygen.org/GLYDS000481. ...", "filename": "human_proteoform_citations_glycosylation_literature_mining.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Proteoform", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "O00300-1...", "..." ], [ "O14672-1...", "..." ] ], "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" } ], [ "O00300-1", "", "Deletion of aspartate 182 in OPG causes juvenile Paget's disease by impairing both protein secretion and binding to RANKL.", "Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research", "2006 Mar", "Middleton-Hardie C, Zhu Q, Cundy H, Lin JM, Callon K, Tong PC, Xu J, Grey A, Cornish J, Naot D", "protein_xref_pubmed", "16491292", "protein_xref_automatic_literature_mining", "16491292" ], [ "O14672-1", "", "Functional role of N-glycosylation from ADAM10 in processing, localization and activity of the enzyme.", "Biochimica et biophysica acta", "2008 Jun", "Escrevente C, Morais VA, Keller S, Soares CM, Altevogt P, Costa J", "protein_xref_pubmed", "18381078", "protein_xref_automatic_literature_mining", "18381078" ], [ "O14773-1", "", "N-glycosylation is crucial for folding, trafficking, and stability of human tripeptidyl-peptidase I.", "The Journal of biological chemistry", "2004 Mar 26", "Wujek P, Kida E, Walus M, Wisniewski KE, Golabek AA", "protein_xref_pubmed", "14702339", "protein_xref_automatic_literature_mining", "14702339" ], [ "O14786-1", "", "A Novel Physiological Glycosaminoglycan-Deficient Splice Variant of Neuropilin-1 Is Anti-Tumorigenic In Vitro and In Vivo.", "PloS one", "2016", "Hendricks C, Dubail J, Brohee L, Delforge Y, Colige A, Deroanne C", "protein_xref_pubmed", "27798666", "protein_xref_automatic_literature_mining", "27798666" ], [ "O15431-1", "", "O-linked glycosylation at threonine 27 protects the copper transporter hCTR1 from proteolytic cleavage in mammalian cells.", "The Journal of biological chemistry", "2007 Jul 13", "Maryon EB, Molloy SA, Kaplan JH", "protein_xref_pubmed", "17525160", "protein_xref_automatic_literature_mining", "17525160" ], [ "O15431-1", "", "Human copper transporter 1 lacking O-linked glycosylation is proteolytically cleaved in a Rab9-positive endosomal compartment.", "The Journal of biological chemistry", "2009 Oct 9", "Maryon EB, Zhang J, Jellison JW, Kaplan JH", "protein_xref_pubmed", "19684018", "protein_xref_automatic_literature_mining", "19684018" ], [ "O60911-1", "", "Determination of cathepsin V activity and intracellular trafficking by N-glycosylation.", "FEBS letters", "2012 Oct 19", "Niwa Y, Suzuki T, Dohmae N, Umezawa K, Simizu S", "protein_xref_pubmed", "22967898", "protein_xref_automatic_literature_mining", "22967898" ], [ "O75355-1", "", "Asparagine 81, an invariant glycosylation site near apyrase conserved region 1, is essential for full enzymatic activity of ecto-nucleoside triphosphate diphosphohydrolase 3.", "Archives of biochemistry and biophysics", "2003 May 1", "Murphy DM, Kirley TL", "protein_xref_pubmed", "12706347", "protein_xref_automatic_literature_mining", "12706347" ], [ "O75355-1", "", "Conserved lysine 79 is important for activity of ecto-nucleoside triphosphate diphosphohydrolase 3 (NTPDase3).", "Purinergic signalling", "2004 Dec", "Basu S, Murphy-Piedmonte DM, Kirley TL", "protein_xref_pubmed", "18404400", "protein_xref_automatic_literature_mining", "18404400" ], [ "O95255-1", "", "Subcellular localization and N-glycosylation of human ABCC6, expressed in MDCKII cells.", "Biochemical and biophysical research communications", "2003 Aug 22", "Sinko E, Ilias A, Ujhelly O, Homolya L, Scheffer GL, Bergen AA, Sarkadi B, Varadi A", "protein_xref_pubmed", "12901863", "protein_xref_automatic_literature_mining", "12901863" ], [ "O95445-1", "", "Proposed lipocalin fold for apolipoprotein M based on bioinformatics and site-directed mutagenesis.", "FEBS letters", "2001 Jun 15", "Duan J, Dahlback B, Villoutreix BO", "protein_xref_pubmed", "11418126", "protein_xref_automatic_literature_mining", "11418126" ], [ "O95980-1", "", "RECK-mediated suppression of tumor cell invasion is regulated by glycosylation in human tumor cell lines.", "Cancer research", "2005 Aug 15", "Simizu S, Takagi S, Tamura Y, Osada H", "protein_xref_pubmed", "16103099", "protein_xref_automatic_literature_mining", "16103099" ], [ "P00450-1", "", "Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM.", "Journal of proteomics", "2018 Oct 30", "Ma J, Sanda M, Wei R, Zhang L, Goldman R", "protein_xref_pubmed", "29427759", "protein_xref_automatic_literature_mining", "29427759" ], [ "P00738-1", "", "Glycosylation status of haptoglobin in sera of patients with prostate cancer vs. benign prostate disease or normal subjects.", "International journal of cancer", "2008 Jan 1", "Fujimura T, Shinohara Y, Tissot B, Pang PC, Kurogochi M, Saito S, Arai Y, Sadilek M, Murayama K, Dell A, Nishimura S, Hakomori SI", "protein_xref_pubmed", "17803183", "protein_xref_automatic_literature_mining", "17803183" ], [ "P00738-1", "", "Site-specific analysis of N-glycans on haptoglobin in sera of patients with pancreatic cancer: a novel approach for the development of tumor markers.", "International journal of cancer", "2008 May 15", "Nakano M, Nakagawa T, Ito T, Kitada T, Hijioka T, Kasahara A, Tajiri M, Wada Y, Taniguchi N, Miyoshi E", "protein_xref_pubmed", "18214858", "protein_xref_automatic_literature_mining", "18214858" ], [ "P00738-1", "", "Glycoproteomic analysis and molecular modeling of haptoglobin multimers.", "Electrophoresis", "2011 Jun", "Boonyapranai K, Tsai HY, Chen MC, Sriyam S, Sinchaikul S, Phutrakul S, Chen ST", "protein_xref_pubmed", "21692080", "protein_xref_automatic_literature_mining", "21692080" ], [ "P00738-1", "", "alpha1-3/4 fucosylation at Asn 241 of beta-haptoglobin is a novel marker for colon cancer: a combinatorial approach for development of glycan biomarkers.", "International journal of cancer", "2012 May 15", "Park SY, Lee SH, Kawasaki N, Itoh S, Kang K, Hee Ryu S, Hashii N, Kim JM, Kim JY, Hoe Kim J", "protein_xref_pubmed", "21780104", "protein_xref_automatic_literature_mining", "21780104" ], [ "P00738-1", "", "Site-specific and linkage analyses of fucosylated N-glycans on haptoglobin in sera of patients with various types of cancer: possible implication for the differential diagnosis of cancer.", "Glycoconjugate journal", "2016 Jun", "Takahashi S, Sugiyama T, Shimomura M, Kamada Y, Fujita K, Nonomura N, Miyoshi E, Nakano M", "protein_xref_pubmed", "26869352", "protein_xref_automatic_literature_mining", "26869352" ], [ "P00738-1", "", "Characteristic glycopeptides associated with extreme human longevity identified through plasma glycoproteomics.", "Biochimica et biophysica acta. General subjects", "2018 Jun", "Miura Y, Hashii N, Ohta Y, Itakura Y, Tsumoto H, Suzuki J, Takakura D, Abe Y, Arai Y, Toyoda M, Kawasaki N, Hirose N, Endo T", "protein_xref_pubmed", "29580922", "protein_xref_automatic_literature_mining", "29580922" ], [ "P00742-1", "", "The missense Thr211Pro mutation in the factor X activation peptide of a bleeding patient causes molecular defect in the clotting cascade.", "Thrombosis and haemostasis", "2013 Jul", "Ding Q, Shen Y, Yang L, Wang X, Rezaie AR", "protein_xref_pubmed", "23677006", "protein_xref_automatic_literature_mining", "23677006" ], [ "P01009-1", "", "Comprehensive glyco-proteomic analysis of human alpha1-antitrypsin and its charge isoforms.", "Proteomics", "2006 Jun", "Kolarich D, Weber A, Turecek PL, Schwarz HP, Altmann F", "protein_xref_pubmed", "16622833", "protein_xref_automatic_literature_mining", "16622833" ], [ "P01009-1", "", "The analysis of alpha-1-antitrypsin glycosylation with direct LC-MS/MS.", "Electrophoresis", "2018 Sep", "Yin H, An M, So PK, Wong MY, Lubman DM, Yao Z", "protein_xref_pubmed", "29405331", "protein_xref_automatic_literature_mining", "29405331" ], [ "P01009-1", "", "Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM.", "Journal of proteomics", "2018 Oct 30", "Ma J, Sanda M, Wei R, Zhang L, Goldman R", "protein_xref_pubmed", "29427759", "protein_xref_automatic_literature_mining", "29427759" ], [ "P01106-1", "", "c-Myc is glycosylated at threonine 58, a known phosphorylation site and a mutational hot spot in lymphomas.", "The Journal of biological chemistry", "1995 Aug 11", "Chou TY, Hart GW, Dang CV", "protein_xref_pubmed", "7642555", "protein_xref_automatic_literature_mining", "7642555" ], [ "P01106-1", "", "Dynamic interplay between O-glycosylation and O-phosphorylation of nucleocytoplasmic proteins: alternative glycosylation/phosphorylation of THR-58, a known mutational hot spot of c-Myc in lymphomas, is regulated by mitogens.", "The Journal of biological chemistry", "2002 May 24", "Kamemura K, Hayes BK, Comer FI, Hart GW", "protein_xref_pubmed", "11904304", "protein_xref_automatic_literature_mining", "11904304" ], [ "P01591-1", "", "Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM.", "Journal of proteomics", "2018 Oct 30", "Ma J, Sanda M, Wei R, Zhang L, Goldman R", "protein_xref_pubmed", "29427759", "protein_xref_automatic_literature_mining", "29427759" ], [ "P01854-1", "", "Structure and function of IgE myeloma protein VL from an atopic patient.", "International archives of allergy and immunology", "1996 Jun", "Zavazal V, Krauz V, Kratzin H, Hilschmann N", "protein_xref_pubmed", "8645991", "protein_xref_automatic_literature_mining", "8645991" ], [ "P02730-1", "", "Calnexin interaction with N-glycosylation mutants of a polytopic membrane glycoprotein, the human erythrocyte anion exchanger 1 (band 3).", "The Journal of biological chemistry", "1999 Jun 18", "Popov M, Reithmeier RA", "protein_xref_pubmed", "10364201", "protein_xref_automatic_literature_mining", "10364201" ], [ "P02730-1", "", "Topology studies with biosynthetic fragments identify interacting transmembrane regions of the human red-cell anion exchanger (band 3; AE1).", "The Biochemical journal", "1999 Dec 15", "Groves JD, Tanner MJ", "protein_xref_pubmed", "10585855", "protein_xref_automatic_literature_mining", "10585855" ], [ "P02730-1", "", "Processing of N-linked oligosaccharide depends on its location in the anion exchanger, AE1, membrane glycoprotein.", "The Biochemical journal", "2000 Jul 1", "Li J, Quilty J, Popov M, Reithmeier RA", "protein_xref_pubmed", "10861210", "protein_xref_automatic_literature_mining", "10861210" ], [ "P02730-1", "", "Topology of the anion exchange protein AE1: the controversial sidedness of lysine 743.", "Biochemistry", "2002 Mar 12", "Kuma H, Shinde AA, Howren TR, Jennings ML", "protein_xref_pubmed", "11876646", "protein_xref_automatic_literature_mining", "11876646" ], [ "P02730-1", "", "Membrane integration and topology of the first transmembrane segment in normal and Southeast Asian ovalocytosis human erythrocyte anion exchanger 1.", "Molecular membrane biology", "2005 May-Jun", "Cheung JC, Reithmeier RA", "protein_xref_pubmed", "16096263", "protein_xref_automatic_literature_mining", "16096263" ], [ "P02786-1", "", "The critical glycosylation site of human transferrin receptor contains a high-mannose oligosaccharide.", "Glycobiology", "1995 Mar", "Hayes GR, Williams A, Costello CE, Enns CA, Lucas JJ", "protein_xref_pubmed", "7780197", "protein_xref_automatic_literature_mining", "7780197" ], [ "P02786-1", "", "Structure of human transferrin receptor oligosaccharides: conservation of site-specific processing.", "Biochemistry", "1997 Apr 29", "Hayes GR, Williams AM, Lucas JJ, Enns CA", "protein_xref_pubmed", "9136890", "protein_xref_automatic_literature_mining", "9136890" ], [ "P02786-1", "", "Effect of glycosylation on the function of a soluble, recombinant form of the transferrin receptor.", "Biochemistry", "2006 May 30", "Byrne SL, Leverence R, Klein JS, Giannetti AM, Smith VC, MacGillivray RT, Kaltashov IA, Mason AB", "protein_xref_pubmed", "16716077", "protein_xref_automatic_literature_mining", "16716077" ], [ "P02786-1", "", "Identification of the O-linked glycosylation site of the human transferrin receptor.", "Glycobiology", "1992 Aug", "Hayes GR, Enns CA, Lucas JJ", "protein_xref_pubmed", "1421757", "protein_xref_automatic_literature_mining", "1421757" ], [ "P02787-1", "", "N-glycosylation at Asn(491) in the Asn-Xaa-Cys motif of human transferrin.", "FEBS letters", "2004 Oct 8", "Satomi Y, Shimonishi Y, Takao T", "protein_xref_pubmed", "15474009", "protein_xref_automatic_literature_mining", "15474009" ], [ "P02787-1", "", "Site-specific carbohydrate profiling of human transferrin by nano-flow liquid chromatography/electrospray ionization mass spectrometry.", "Rapid communications in mass spectrometry : RCM", "2004", "Satomi Y, Shimonishi Y, Hase T, Takao T", "protein_xref_pubmed", "15536627", "protein_xref_automatic_literature_mining", "15536627" ], [ "P02787-1", "", "Structural change of N-glycan exposes hydrophobic surface of human transferrin.", "Glycobiology", "2014 Aug", "Nagae M, Morita-Matsumoto K, Arai S, Wada I, Matsumoto Y, Saito K, Hashimoto Y, Yamaguchi Y", "protein_xref_pubmed", "24780636", "protein_xref_automatic_literature_mining", "24780636" ], [ "P02787-1", "", "In situ visualization of a glycoform of transferrin: localization of alpha2,6-sialylated transferrin in the liver.", "Journal of biochemistry", "2015 Apr", "Matsumoto Y, Saito T, Hoshi K, Ito H, Kariya Y, Nagae M, Yamaguchi Y, Hagiwara Y, Kinoshita N, Wada I, Saito K, Honda T, Hashimoto Y", "protein_xref_pubmed", "25425657", "protein_xref_automatic_literature_mining", "25425657" ], [ "P02787-1", "", "Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM.", "Journal of proteomics", "2018 Oct 30", "Ma J, Sanda M, Wei R, Zhang L, Goldman R", "protein_xref_pubmed", "29427759", "protein_xref_automatic_literature_mining", "29427759" ], [ "P02790-1", "", "Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM.", "Journal of proteomics", "2018 Oct 30", "Ma J, Sanda M, Wei R, Zhang L, Goldman R", "protein_xref_pubmed", "29427759", "protein_xref_automatic_literature_mining", "29427759" ], [ "P03956-1", "", "N-glycan structures of matrix metalloproteinase-1 derived from human fibroblasts and from HT-1080 fibrosarcoma cells.", "European journal of biochemistry", "1999 Feb", "Saarinen J, Welgus HG, Flizar CA, Kalkkinen N, Helin J", "protein_xref_pubmed", "10092871", "protein_xref_automatic_literature_mining", "10092871" ], [ "P04004-1", "", "Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM.", "Journal of proteomics", "2018 Oct 30", "Ma J, Sanda M, Wei R, Zhang L, Goldman R", "protein_xref_pubmed", "29427759", "protein_xref_automatic_literature_mining", "29427759" ], [ "P04070-1", "", "Purification of protein C from canine plasma.", "BMC veterinary research", "2014 Oct 18", "Wong VM, Bienzle D, Hayes MA, Taylor P, Wood RD", "protein_xref_pubmed", "25326145", "protein_xref_automatic_literature_mining", "25326145" ], [ "P04275-1", "", "N-linked glycosylation of VWF modulates its interaction with ADAMTS13.", "Blood", "2008 Mar 15", "McKinnon TA, Chion AC, Millington AJ, Lane DA, Laffan MA", "protein_xref_pubmed", "17975018", "protein_xref_automatic_literature_mining", "17975018" ], [ "P04275-1", "", "Mapping the N-glycome of human von Willebrand factor.", "The Biochemical journal", "2012 Oct 15", "Canis K, McKinnon TA, Nowak A, Haslam SM, Panico M, Morris HR, Laffan MA, Dell A", "protein_xref_pubmed", "22849435", "protein_xref_automatic_literature_mining", "22849435" ], [ "P04275-1", "", "N-linked glycan stabilization of the VWF A2 domain.", "Blood", "2016 Mar 31", "Lynch CJ, Lane DA", "protein_xref_pubmed", "26773038", "protein_xref_automatic_literature_mining", "26773038" ], [ "P04275-1", "", "Site-specific analysis of von Willebrand factor O-glycosylation.", "Journal of thrombosis and haemostasis : JTH", "2016 Apr", "Solecka BA, Weise C, Laffan MA, Kannicht C", "protein_xref_pubmed", "26784534", "protein_xref_automatic_literature_mining", "26784534" ], [ "P05155-1", "", "Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM.", "Journal of proteomics", "2018 Oct 30", "Ma J, Sanda M, Wei R, Zhang L, Goldman R", "protein_xref_pubmed", "29427759", "protein_xref_automatic_literature_mining", "29427759" ], [ "P05186-1", "", "Glycosylation-deficient mutations in tissue-nonspecific alkaline phosphatase impair its structure and function and are linked to infantile hypophosphatasia.", "The FEBS journal", "2016 Mar", "Komaru K, Satou Y, Al-Shawafi HA, Numa-Kinjoh N, Sohda M, Oda K", "protein_xref_pubmed", "26797772", "protein_xref_automatic_literature_mining", "26797772" ], [ "P05231-1", "", "N-linked glycosylation is required for optimal function of Kaposi's sarcoma herpesvirus-encoded, but not cellular, interleukin 6.", "The Journal of experimental medicine", "2004 Feb 16", "Dela Cruz CS, Lee Y, Viswanathan SR, El-Guindy AS, Gerlach J, Nikiforow S, Shedd D, Gradoville L, Miller G", "protein_xref_pubmed", "14970177", "protein_xref_automatic_literature_mining", "14970177" ], [ "P06280-1", "", "Human alpha-galactosidase A: glycosylation site 3 is essential for enzyme solubility.", "The Biochemical journal", "1998 Jun 15", "Ioannou YA, Zeidner KM, Grace ME, Desnick RJ", "protein_xref_pubmed", "9620884", "protein_xref_automatic_literature_mining", "9620884" ], [ "P07196-1", "", "Cytoplasmic O-GlcNAc modification of the head domain and the KSP repeat motif of the neurofilament protein neurofilament-H.", "The Journal of biological chemistry", "1996 Aug 23", "Dong DL, Xu ZS, Hart GW, Cleveland DW", "protein_xref_pubmed", "8702840", "protein_xref_automatic_literature_mining", "8702840" ], [ "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_automatic_literature_mining", "25327667" ], [ "P07288-1", "", "Characterization of the Glycosylation Site of Human PSA Prompted by Missense Mutation using LC-MS/MS.", "Journal of proteome research", "2015 Jul 2", "Song E, Hu Y, Hussein A, Yu CY, Tang H, Mechref Y", "protein_xref_pubmed", "26022737", "protein_xref_automatic_literature_mining", "26022737" ], [ "P08473-1", "", "The human CD10 lacking an N-glycan at Asn(628) is deficient in surface expression and neutral endopeptidase activity.", "Biochimica et biophysica acta", "2012 Nov", "Sato B, Katagiri YU, Iijima K, Yamada H, Ito S, Kawasaki N, Okita H, Fujimoto J, Kiyokawa N", "protein_xref_pubmed", "22766194", "protein_xref_automatic_literature_mining", "22766194" ], [ "P08575-3", "", "Regulation of galectin-3-induced apoptosis of Jurkat cells by both O-glycans and N-glycans on CD45.", "FEBS letters", "2013 Dec 11", "Xue J, Gao X, Fu C, Cong Z, Jiang H, Wang W, Chen T, Wei Q, Qin C", "protein_xref_pubmed", "24211831", "protein_xref_automatic_literature_mining", "24211831" ], [ "P08842-1", "", "Effects of mutations and glycosylations on STS activity: a site-directed mutagenesis study.", "Molecular and cellular endocrinology", "2008 Feb 13", "Stengel C, Newman SP, Day JM, Tutill HJ, Reed MJ, Purohit A", "protein_xref_pubmed", "18180093", "protein_xref_automatic_literature_mining", "18180093" ], [ "P10909-1", "", "Clusterin glycopeptide variant characterization reveals significant site-specific glycan changes in the plasma of clear cell renal cell carcinoma.", "Journal of proteome research", "2015 Jun 5", "Gbormittah FO, Bones J, Hincapie M, Tousi F, Hancock WS, Iliopoulos O", "protein_xref_pubmed", "25855029", "protein_xref_automatic_literature_mining", "25855029" ], [ "P10909-1", "", "Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM.", "Journal of proteomics", "2018 Oct 30", "Ma J, Sanda M, Wei R, Zhang L, Goldman R", "protein_xref_pubmed", "29427759", "protein_xref_automatic_literature_mining", "29427759" ], [ "P11279-1", "", "Assignment of O-glycan attachment sites to the hinge-like regions of human lysosomal membrane glycoproteins lamp-1 and lamp-2.", "Archives of biochemistry and biophysics", "1993 Jul", "Carlsson SR, Lycksell PO, Fukuda M", "protein_xref_pubmed", "8323299", "protein_xref_automatic_literature_mining", "8323299" ], [ "P11678-1", "", "The status of half-cystine residues and locations of N-glycosylated asparagine residues in human eosinophil peroxidase.", "Archives of biochemistry and biophysics", "2000 Jul 1", "Thomsen AR, Sottrup-Jensen L, Gleich GJ, Oxvig C", "protein_xref_pubmed", "10864452", "protein_xref_automatic_literature_mining", "10864452" ], [ "P13497-1", "", "Post-translational modification of bone morphogenetic protein-1 is required for secretion and stability of the protein.", "The Journal of biological chemistry", "2002 Nov 8", "Garrigue-Antar L, Hartigan N, Kadler KE", "protein_xref_pubmed", "12218058", "protein_xref_automatic_literature_mining", "12218058" ], [ "P15289-1", "", "Glycosylation and phosphorylation of arylsulfatase A.", "The Journal of biological chemistry", "1994 Aug 19", "Sommerlade HJ, Selmer T, Ingendoh A, Gieselmann V, von Figura K, Neifer K, Schmidt B", "protein_xref_pubmed", "7914890", "protein_xref_automatic_literature_mining", "7914890" ], [ "P15382-1", "", "O-glycosylation of the cardiac I(Ks) complex.", "The Journal of physiology", "2011 Aug 1", "Chandrasekhar KD, Lvov A, Terrenoire C, Gao GY, Kass RS, Kobertz WR", "protein_xref_pubmed", "21669976", "protein_xref_automatic_literature_mining", "21669976" ], [ "P16473-1", "", "Site-directed mutagenesis of the human thyrotropin receptor: role of asparagine-linked oligosaccharides in the expression of a functional receptor.", "Molecular endocrinology (Baltimore, Md.)", "1991 Jan", "Russo D, Chazenbalk GD, Nagayama Y, Wadsworth HL, Rapoport B", "protein_xref_pubmed", "2017190", "protein_xref_automatic_literature_mining", "2017190" ], [ "P16662-1", "", "The effects of N-glycosylation on the glucuronidation of zidovudine and morphine by UGT2B7 expressed in HEK293 cells.", "Drug metabolism and pharmacokinetics", "2012", "Nagaoka K, Hanioka N, Ikushiro S, Yamano S, Narimatsu S", "protein_xref_pubmed", "22240840", "protein_xref_automatic_literature_mining", "22240840" ], [ "P16671-1", "", "The Human Scavenger Receptor CD36: glycosylation status and its role in trafficking and function.", "The Journal of biological chemistry", "2009 Jun 12", "Hoosdally SJ, Andress EJ, Wooding C, Martin CA, Linton KJ", "protein_xref_pubmed", "19369259", "protein_xref_automatic_literature_mining", "19369259" ], [ "P19634-1", "", "The Na+/H+ exchanger NHE-1 possesses N- and O-linked glycosylation restricted to the first N-terminal extracellular domain.", "Biochemistry", "1994 Aug 30", "Counillon L, Pouyssegur J, Reithmeier RA", "protein_xref_pubmed", "8068684", "protein_xref_automatic_literature_mining", "8068684" ], [ "P19801-1", "", "Oligomannosidic glycans at Asn-110 are essential for secretion of human diamine oxidase.", "The Journal of biological chemistry", "2018 Jan 19", "Gludovacz E, Maresch D, Lopes de Carvalho L, Puxbaum V, Baier LJ, Sutzl L, Guedez G, Grunwald-Gruber C, Ulm B, Pils S, Ristl R, Altmann F, Jilma B, Salminen TA, Borth N, Boehm T", "protein_xref_pubmed", "29187599", "protein_xref_automatic_literature_mining", "29187599" ], [ "P20827-1", "", "Biological and structural characterization of glycosylation on ephrin-A1, a preferred ligand for EphA2 receptor tyrosine kinase.", "The Journal of biological chemistry", "2013 Jun 21", "Ferluga S, Hantgan R, Goldgur Y, Himanen JP, Nikolov DB, Debinski W", "protein_xref_pubmed", "23661698", "protein_xref_automatic_literature_mining", "23661698" ], [ "P20933-1", "", "Glycosylation and phosphorylation of lysosomal glycosylasparaginase.", "Archives of biochemistry and biophysics", "1996 Apr 1", "Park H, Vettese-Dadey M, Aronson NN Jr", "protein_xref_pubmed", "8638940", "protein_xref_automatic_literature_mining", "8638940" ], [ "P21217-1", "", "The C-terminal N-glycosylation sites of the human alpha1,3/4-fucosyltransferase III, -V, and -VI (hFucTIII, -V, adn -VI) are necessary for the expression of full enzyme activity.", "Glycobiology", "2000 Sep", "Christensen LL, Jensen UB, Bross P, Orntoft TF", "protein_xref_pubmed", "10988254", "protein_xref_automatic_literature_mining", "10988254" ], [ "P25103-1", "", "Functional consequences of alteration of N-linked glycosylation sites on the neurokinin 1 receptor.", "Proceedings of the National Academy of Sciences of the United States of America", "2007 Jun 19", "Tansky MF, Pothoulakis C, Leeman SE", "protein_xref_pubmed", "17563389", "protein_xref_automatic_literature_mining", "17563389" ], [ "P25116-1", "", "N-linked glycosylation regulates human proteinase-activated receptor-1 cell surface expression and disarming via neutrophil proteinases and thermolysin.", "The Journal of biological chemistry", "2011 Jul 1", "Xiao YP, Morice AH, Compton SJ, Sadofsky L", "protein_xref_pubmed", "21550978", "protein_xref_automatic_literature_mining", "21550978" ], [ "P29965-1", "", "Determination of carbohydrate structures N-linked to soluble CD154 and characterization of the interactions of CD40 with CD154 expressed in Pichia pastoris and Chinese hamster ovary cells.", "Protein expression and purification", "2001 Nov", "Khandekar SS, Silverman C, Wells-Marani J, Bacon AM, Birrell H, Brigham-Burke M, DeMarini DJ, Jonak ZL, Camilleri P, Fishman-Lobell J", "protein_xref_pubmed", "11676606", "protein_xref_automatic_literature_mining", "11676606" ], [ "P33527-1", "", "Membrane topology of the multidrug resistance protein (MRP). A study of glycosylation-site mutants reveals an extracytosolic NH2 terminus.", "The Journal of biological chemistry", "1997 Sep 19", "Hipfner DR, Almquist KC, Leslie EM, Gerlach JH, Grant CE, Deeley RG, Cole SP", "protein_xref_pubmed", "9295302", "protein_xref_automatic_literature_mining", "9295302" ], [ "P34998-1", "", "N-glycosylation of CRF receptor type 1 is important for its ligand-specific interaction.", "American journal of physiology. Endocrinology and metabolism", "2001 Nov", "Assil IQ, Abou-Samra AB", "protein_xref_pubmed", "11595658", "protein_xref_automatic_literature_mining", "11595658" ], [ "P35052-1", "", "The structural role of N-linked glycans on human glypican-1.", "Biochemistry", "2011 Nov 1", "Svensson G, Hyrenius Wittsten A, Linse S, Mani K", "protein_xref_pubmed", "21932778", "protein_xref_automatic_literature_mining", "21932778" ], [ "P35222-1", "", "beta-catenin is O-GlcNAc glycosylated at Serine 23: implications for beta-catenin's subcellular localization and transactivator function.", "Experimental cell research", "2014 Feb 15", "Ha JR, Hao L, Venkateswaran G, Huang YH, Garcia E, Persad S", "protein_xref_pubmed", "24342833", "protein_xref_automatic_literature_mining", "24342833" ], [ "P35354-1", "", "Investigation of human cyclooxygenase-2 glycosylation heterogeneity and protein expression in insect and mammalian cell expression systems.", "Protein expression and purification", "1997 Apr", "Percival MD, Bastien L, Griffin PR, Kargman S, Ouellet M, O'Neill GP", "protein_xref_pubmed", "9126611", "protein_xref_automatic_literature_mining", "9126611" ], [ "P35354-1", "", "Characterization of the glycosylation sites in cyclooxygenase-2 using mass spectrometry.", "Biochemistry", "2001 Mar 13", "Nemeth JF, Hochgesang GP Jr, Marnett LJ, Caprioli RM", "protein_xref_pubmed", "11258925", "protein_xref_automatic_literature_mining", "11258925" ], [ "P35354-1", "", "Glycosylation of human cyclooxygenase-2 (COX-2) decreases the efficacy of certain COX-2 inhibitors.", "Pharmacological research", "2012 Apr", "Sevigny MB, Graham K, Ponce E, Louie MC, Mitchell K", "protein_xref_pubmed", "22245433", "protein_xref_automatic_literature_mining", "22245433" ] ] }, "readme": "Name\n - Human Proteoform Citations (Literature Mining)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2020-06-26T15:29:27.375356\n\nModified on\n - 2021-06-04T09:49:02.580309\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@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\nUsability Domain\n - The dataset provides citation details corresponding to the PubMed ID (PMID) from file https://data.glygen.org/GLYDS000481. The script accesses the NCBI ENTREZ infrastructure to retrieve the publication information of the given PMID.\n\nDescription Domain\n Keywords\n - PMID\n - journal\n - citations\n - authors\n - Literature\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_literature_mining.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/human_proteoform_glycosylation_sites_literature_mining.csv\n Output Subdomain\n Name: human_proteoform_citations_glycosylation_literature_mining.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/human_proteoform_citations_glycosylation_literature_mining.csv\n Name: human_proteoform_citations_glycosylation_literature_mining.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/human_proteoform_citations_glycosylation_literature_mining.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_literature_mining.csv" }