{ "bcoid": "GLY_000517", "title": "Human O-GlcNAc Glycosylation Sites (MCW)", "description": "The Human O-GlcNAc Glycosylation Sites (MCW) contains human (taxid:9606) O-GlcNAc modifications on Serine ...", "filename": "human_proteoform_glycosylation_sites_o_glcnac_mcw.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Proteoform", "tags": "O-GlcNAc Glycosylation Sites (MCW)", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "A0A075B759-1...", "..." ], [ "A0A075B759-1...", "..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" }, { "type": "string", "label": "o_glcnac_score" }, { "type": "string", "label": "sites_bonus" }, { "type": "string", "label": "disclaimer" }, { "type": "string", "label": "o_glcnac_sites" }, { "type": "string", "label": "column1" }, { "type": "string", "label": "number_of_references" }, { "type": "string", "label": "ms_based_lc_etd_hcd_cad_ms_ms" }, { "type": "string", "label": "labeling_enzymatic_&_metabolic" }, { "type": "string", "label": "ip_based" }, { "type": "string", "label": "lectin_based" }, { "type": "string", "label": "in_vitro_o_glcnacylation" }, { "type": "string", "label": "ogt_nanobody" }, { "type": "string", "label": "count_techniques" }, { "type": "string", "label": "notes" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "carb_name" }, { "type": "string", "label": "glycosylation_subtype" }, { "type": "string", "label": "status" }, { "type": "string", "label": "uniprotkb_id" }, { "type": "string", "label": "gene_name" }, { "type": "string", "label": "recommended_name_full" }, { "type": "string", "label": "peptide" } ], [ "A0A075B759-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A0A075B759", "protein_xref_oglcnac_db", "A0A075B759", "3", "0", "0", "", "0", "1", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "PAL4E_HUMAN", "PPIAL4E", "Peptidyl-prolyl cis-trans isomerase A-like 4E", "" ], [ "A0A075B759-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "30444036", "protein_xref_oglcnac_db", "A0A075B759", "3", "0", "0", "", "0", "1", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "PAL4E_HUMAN", "PPIAL4E", "Peptidyl-prolyl cis-trans isomerase A-like 4E", "" ], [ "A0A0B4J2D5-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A0A0B4J2D5", "protein_xref_oglcnac_db", 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"0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "UBA6_HUMAN", "UBA6", "Ubiquitin-like modifier-activating enzyme 6", "LIVDF-S-NPEAP" ], [ "A0AVT1-1", "317", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "23301498", "protein_xref_oglcnac_db", "A0AVT1", "20", "15", "0", "S317", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "UBA6_HUMAN", "UBA6", "Ubiquitin-like modifier-activating enzyme 6", "LIVDF-S-NPEAP" ], [ "A0AVT1-1", "317", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A0AVT1", "protein_xref_oglcnac_db", "A0AVT1", "20", "15", "0", "S317", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "UBA6_HUMAN", "UBA6", "Ubiquitin-like modifier-activating enzyme 6", "LIVDF-S-NPEAP" ], [ "A0AVT1-1", "317", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "28510447", "protein_xref_oglcnac_db", "A0AVT1", "20", "15", "0", "S317", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "UBA6_HUMAN", "UBA6", "Ubiquitin-like modifier-activating enzyme 6", "LIVDF-S-NPEAP" ], [ "A0AVT1-1", "317", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A0AVT1", "protein_xref_oglcnac_db", "A0AVT1", "20", "15", "0", "S317", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "UBA6_HUMAN", "UBA6", "Ubiquitin-like modifier-activating enzyme 6", "LIVDF-S-NPEAP" ], [ "A0AVT1-1", "317", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "29351928", "protein_xref_oglcnac_db", "A0AVT1", "20", "15", "0", "S317", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "UBA6_HUMAN", "UBA6", "Ubiquitin-like modifier-activating enzyme 6", "LIVDF-S-NPEAP" ], [ "A0FGR8-1", "758", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A0FGR8", "protein_xref_oglcnac_db", "A0FGR8", "20", "15", "0", "S758", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "ESYT2_HUMAN", "ESYT2", "Extended synaptotagmin-2", "TPSIA-S-DISLP" ], [ "A0FGR8-1", "758", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "28411811", "protein_xref_oglcnac_db", "A0FGR8", "20", "15", "0", "S758", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "ESYT2_HUMAN", "ESYT2", "Extended synaptotagmin-2", "TPSIA-S-DISLP" ], [ "A0FGR8-1", "758", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A0FGR8", "protein_xref_oglcnac_db", "A0FGR8", "20", "15", "0", "S758", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "ESYT2_HUMAN", "ESYT2", "Extended synaptotagmin-2", "TPSIA-S-DISLP" ], [ "A0FGR8-1", "758", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "29351928", "protein_xref_oglcnac_db", "A0FGR8", "20", "15", "0", "S758", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "ESYT2_HUMAN", "ESYT2", "Extended synaptotagmin-2", "TPSIA-S-DISLP" ], [ "A0FGR8-1", "758", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A0FGR8", "protein_xref_oglcnac_db", "A0FGR8", "20", "15", "0", "S758", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "ESYT2_HUMAN", "ESYT2", "Extended synaptotagmin-2", "TPSIA-S-DISLP" ], [ "A0FGR8-1", "758", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "28510447", "protein_xref_oglcnac_db", "A0FGR8", "20", "15", "0", "S758", "0", "3", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "ESYT2_HUMAN", "ESYT2", "Extended synaptotagmin-2", "TPSIA-S-DISLP" ], [ "A0MZ66-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A0MZ66", "protein_xref_oglcnac_db", "A0MZ66", "4", "0", "0", "", "0", "2", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SHOT1_HUMAN", "SHTN1", "Shootin-1", "" ], [ "A0MZ66-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "23301498", "protein_xref_oglcnac_db", "A0MZ66", "4", "0", "0", "", "0", "2", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SHOT1_HUMAN", "SHTN1", "Shootin-1", "" ], [ "A0MZ66-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A0MZ66", "protein_xref_oglcnac_db", "A0MZ66", "4", "0", "0", "", "0", "2", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SHOT1_HUMAN", "SHTN1", "Shootin-1", "" ], [ "A0MZ66-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "28510447", "protein_xref_oglcnac_db", "A0MZ66", "4", "0", "0", "", "0", "2", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SHOT1_HUMAN", "SHTN1", "Shootin-1", "" ], [ "A1A5D9-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A1A5D9", "protein_xref_oglcnac_db", "A1A5D9", "2", "0", "0", "", "0", "1", "1", "0", "0", "0", "0", "0", "1", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "BICL2_HUMAN", "BICDL2", "BICD family-like cargo adapter 2", "" ], [ "A1A5D9-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "28411811", "protein_xref_oglcnac_db", "A1A5D9", "2", "0", "0", "", "0", "1", "1", "0", "0", "0", "0", "0", "1", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "BICL2_HUMAN", "BICDL2", "BICD family-like cargo adapter 2", "" ], [ "A1E959-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A1E959", "protein_xref_oglcnac_db", "A1E959", "2", "0", "0", "", "0", "1", "1", "0", "0", "0", "0", "0", "1", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "ODAM_HUMAN", "ODAM", "Odontogenic ameloblast-associated protein", "" ], [ "A1E959-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "28411811", "protein_xref_oglcnac_db", "A1E959", "2", "0", "0", "", "0", "1", "1", "0", "0", "0", "0", "0", "1", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "ODAM_HUMAN", "ODAM", "Odontogenic ameloblast-associated protein", "" ], [ "A1L020-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A1L020", "protein_xref_oglcnac_db", "A1L020", "3", "0", "0", "", "0", "1", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "MEX3A_HUMAN", "MEX3A", "RNA-binding protein MEX3A", "" ], [ "A1L020-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "23301498", "protein_xref_oglcnac_db", "A1L020", "3", "0", "0", "", "0", "1", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "MEX3A_HUMAN", "MEX3A", "RNA-binding protein MEX3A", "" ], [ "A1L0T0-1", "121", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A1L0T0", "protein_xref_oglcnac_db", "A1L0T0", "18", "15", "0", "T121", "0", "1", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "HACL2_HUMAN", "ILVBL", "2-hydroxyacyl-CoA lyase 2", "GVAAV-T-AGPGL" ], [ "A1L0T0-1", "121", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "29351928", "protein_xref_oglcnac_db", "A1L0T0", "18", "15", "0", "T121", "0", "1", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "HACL2_HUMAN", "ILVBL", "2-hydroxyacyl-CoA lyase 2", "GVAAV-T-AGPGL" ], [ "A1L188-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A1L188", "protein_xref_oglcnac_db", "A1L188", "3", "0", "0", "", "0", "1", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "NDUF8_HUMAN", "NDUFAF8", "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 8", "" ], [ "A1L188-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "28510447", "protein_xref_oglcnac_db", "A1L188", "3", "0", "0", "", "0", "1", "1", "1", "0", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "NDUF8_HUMAN", "NDUFAF8", "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 8", "" ], [ "A1L4H1-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A1L4H1", "protein_xref_oglcnac_db", "A1L4H1", "2", "0", "0", "", "0", "1", "1", "0", "0", "0", "0", "0", "1", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SRCRL_HUMAN", "SSC5D", "Soluble scavenger receptor cysteine-rich domain-containing protein SSC5D", "" ], [ "A1L4H1-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "28411811", "protein_xref_oglcnac_db", "A1L4H1", "2", "0", "0", "", "0", "1", "1", "0", "0", "0", "0", "0", "1", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SRCRL_HUMAN", "SSC5D", "Soluble scavenger receptor cysteine-rich domain-containing protein SSC5D", "" ], [ "A2A3N6-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A3N6", "protein_xref_oglcnac_db", "A2A3N6", "3", "0", "0", "", "0", "1", "1", "0", "1", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "PIPSL_HUMAN", "PIPSL", "Putative PIP5K1A and PSMD4-like protein", "" ], [ "A2A3N6-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "20305658", "protein_xref_oglcnac_db", "A2A3N6", "3", "0", "0", "", "0", "1", "1", "0", "1", "0", "0", "0", "2", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "PIPSL_HUMAN", "PIPSL", "Putative PIP5K1A and PSMD4-like protein", "" ], [ "A2RTX5-1", "", "", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2RTX5", "protein_xref_oglcnac_db", "A2RTX5", "2", "0", "0", "", "0", "1", "1", "0", "0", "0", "0", "0", "1", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SYTC2_HUMAN", "TARS3", "Threonine--tRNA ligase 2, cytoplasmic", "" ], [ "A2RTX5-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "28411811", 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"T108/T112/T113/T126/T127/S129/T130/S133/S135/T138", "0", "7", "1", "1", "0", "0", "0", "1", "3", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SBNO1_HUMAN", "SBNO1", "Protein strawberry notch homolog 1", "KTPPV-T-TNRQT" ], [ "A3KN83-1", "112", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A3KN83", "protein_xref_oglcnac_db", "A3KN83", "25", "15", "0", "T108/T112/T113/T126/T127/S129/T130/S133/S135/T138", "0", "7", "1", "1", "0", "0", "0", "1", "3", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SBNO1_HUMAN", "SBNO1", "Protein strawberry notch homolog 1", "KTPPV-T-TNRQT" ], [ "A3KN83-1", "112", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "29351928", "protein_xref_oglcnac_db", "A3KN83", "25", "15", "0", "T108/T112/T113/T126/T127/S129/T130/S133/S135/T138", "0", "7", "1", "1", "0", "0", "0", "1", "3", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SBNO1_HUMAN", "SBNO1", "Protein strawberry notch homolog 1", "KTPPV-T-TNRQT" ], [ "A3KN83-1", "113", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A3KN83", "protein_xref_oglcnac_db", "A3KN83", "25", "15", "0", "T108/T112/T113/T126/T127/S129/T130/S133/S135/T138", "0", "7", "1", "1", "0", "0", "0", "1", "3", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SBNO1_HUMAN", "SBNO1", "Protein strawberry notch homolog 1", "TPPVT-T-NRQTI" ], [ "A3KN83-1", "113", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "20068230", "protein_xref_oglcnac_db", "A3KN83", "25", "15", "0", "T108/T112/T113/T126/T127/S129/T130/S133/S135/T138", "0", "7", "1", "1", "0", "0", "0", "1", "3", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SBNO1_HUMAN", "SBNO1", "Protein strawberry notch homolog 1", "TPPVT-T-NRQTI" ], [ "A3KN83-1", "113", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A3KN83", "protein_xref_oglcnac_db", "A3KN83", "25", "15", "0", "T108/T112/T113/T126/T127/S129/T130/S133/S135/T138", "0", "7", "1", "1", "0", "0", "0", "1", "3", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SBNO1_HUMAN", "SBNO1", "Protein strawberry notch homolog 1", "TPPVT-T-NRQTI" ], [ "A3KN83-1", "113", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "27655845", "protein_xref_oglcnac_db", "A3KN83", "25", "15", "0", "T108/T112/T113/T126/T127/S129/T130/S133/S135/T138", "0", "7", "1", "1", "0", "0", "0", "1", "3", "", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "SBNO1_HUMAN", "SBNO1", "Protein strawberry notch homolog 1", "TPPVT-T-NRQTI" ] ] }, "readme": "Name\n - Human O-GlcNAc Glycosylation Sites (MCW)\n\nVersion\n - 1.8.25\n\nCreated on\n - 2020-07-09T13:50:43.000375\n\nModified on\n - 2021-02-22T19:26:46.446922\n\nCreated by\n - [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - Stephanie Olivier-Van Stichelen [solivier@mcw.edu], Eugenia Wulff-Fuentes [ewulff@mcw.edu], Rex R. Berendt [rberendt@mcw.edu], Logan Massman [lmassman@mcw.edu], Laura Danner [ldanner@mcw.edu]\n\nChecksum\n - \n\nUsability Domain\n - The Human O-GlcNAc Glycosylation Sites (MCW) contains human (taxid:9606) O-GlcNAc modifications on Serine and Threonine extracted from the publication and mapped to the UniProtKB canonical accession and fasta sequence. The GlyTouCan ID for the O-GlcNAc is G49108TO. The dataset also contains other information such as O-GlcNAc score, the count and the techniques used to determine the O-GlcNAc modification and the peptide sequence from the -5 to +5 postion of the modified residue. The dataset also containes disclaimer and notes where the position of sites in publication and in the fasta sequence varies.\n - The current dataset has 4997 proteins with O-GlcNAc modifications. Out of which 3262 proteins have no site information where as 1735 proteins have 6722 sites.\n - The dataset is contributed from The O-GlcNAc Database maintained by Stephanie Olivier's lab \n - Wulff-Fuentes E, Berendt RR, Massman L, Danner L, Malard F, Vora J, Kahsay R, and Olivier-Van Stichelen S, The Human O-GlcNAcome Database and Meta-Analysis. Scientific Data 8, 25 (2021) \n - QC check - The python script is used to process each protein entry of the database table and perform quality control (QC). In the QC checks, the reported UniProtKB accessions in the database are matched with the GlyGen\u2019s human protein master list of UniProtKB canonical accessions to ensure all of the proteins belong to human species. Next, the O-GlcNAc site data that contained the amino acid residue and its position are mapped to the GlyGen\u2019s fasta sequence for the corresponding human UniProtKB canonical proteins. The amino acid residues and positions that don't match with the fasta sequence of the canonical protein were flagged and excluded from the table. Similarly, the protein entries that don't have any site information are also excluded. The entries that passed all the quality control steps are exported as a final csv dataset file whereas the excluded entries are exported in a log file with the reasons for exclusion for further manual verification.\n - DISCLAIMER - For each entry, an O-GlcNAc score was attributed to each O-GlcNAcylated protein, reflecting the confidence in the protein\u2019s O-GlcNAcylation identification. The score combined the number of articles and techniques used and the availability of some O-GlcNAcylation sites. Interestingly, a total of 2,237 proteins had an O-GlcNAc score of 3 or under, meaning that (1) no sites were identified, (2) only one technique was used, and (3) 1-2 articles were associated with the entry. Often identified from large-scale proteomics studies, at least an extra-validation step would be highly recommended to confirm their O-GlcNAcylation.\n - The log file - https://data.glygen.org/ln2data/releases/data/v-1.8.25/logs/human_proteoform_glycosylation_sites_o_glcnac_mcw.log contains the entries that were excluded from the output file along with the reason for exclusion.\n - The orginal unprocessed dataset in excel format can be found at https://figshare.com/articles/The_human_O-GlcNAcome_database/12443495/4\n\nDescription Domain\n Keywords\n - O-GlcNAc\n\n Pipeline Steps\n - Step-1: The script maps the UniProtKB accesions to the UniProtKB Canonical accessions and also checks the position and amino acid of O-GlcNAc modified residue against UniProtKB Canonical sequences. The script that processes this dataset matches the amino acid and position with the latest release fasta file as a QC check to eliminate the incorrect entries. The script also adds the -5 and +5 amino acids from the modified residue in the peptide field.\n\nExecution Domain\n Scripts - https://github.com/glygener/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_o-glcnacome_mcw.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/source/human_o-glcnacome_mcw.csv\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_protein_masterlist.csv\n Name: human_protein_allsequences.fasta\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_protein_allsequences.fasta\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_o_glcnac_mcw.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_proteoform_glycosylation_sites_o_glcnac_mcw.csv\n Name: human_proteoform_glycosylation_sites_o_glcnac_mcw.log\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/logs/human_proteoform_glycosylation_sites_o_glcnac_mcw.log\n Name: human_proteoform_glycosylation_sites_o_glcnac_mcw.stat.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/human_proteoform_glycosylation_sites_o_glcnac_mcw.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.25/reviewed/human_proteoform_glycosylation_sites_o_glcnac_mcw.csv" }