{ "bcoid": "GLY_001051", "title": "Human blood platelet Glycosylation Sites", "description": "The Human blood platelet Glycosylation Sites dataset contains glycosylation sites of thrombin-treated ...", "filename_list": "human_proteoform_glycosylation_sites_platelet.csv", "filename": "human_proteoform_glycosylation_sites_platelet.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Proteoform" ], "tag": [ "O-Glucosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P07996-1...", "580..." ], [ "Q14766-1...", "801..." ] ], "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": "glycosylation_subtype" }, { "type": "string", "label": "site_type" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "start_aa" }, { "type": "string", "label": "end_aa" }, { "type": "string", "label": "composition" }, { "type": "string", "label": "peptide" }, { "type": "string", "label": "peptide_start_pos" }, { "type": "string", "label": "peptide_end_pos" }, { "type": "string", "label": "site_seq" }, { "type": "string", "label": "notes" } ], [ "P07996-1", "580", "Ser", "G29068FM", "O-linked", "protein_xref_pubmed", "38237698", "protein_xref_data_submission", "GLY_001051", "", "known", "580", "580", "S", "S", "HexNAc(1)", "CGACPPGYSGNGIQCTDVDECKEVPDACFNHNGEHR", "572", "607", "S", "Thrombin-activated platelet releasate proteins were found to be enriched for a wide range of O-glycan modifications. Some C-mannosylation glycosylation sites were also identified." ], [ "Q14766-1", "801", "Thr", "G23729WG", "O-linked", "protein_xref_pubmed", "38237698", "protein_xref_data_submission", "GLY_001051", "", "known", "801", "801", "T", "T", "HexNAc(1)Hex(1)NeuAc(2)", "EHGPGVAEPEVATAPPEKEIPSLDQEK", "789", "815", "T", "Thrombin-activated platelet releasate proteins were found to be enriched for a wide range of O-glycan modifications. Some C-mannosylation glycosylation sites were also identified." ] ] }, "readme": "Name\n - Human blood platelet Glycosylation Sites\n\nVersion\n - v-2.8.1\n\nCreated on\n - 2024-08-01T12:27:42\n\nModified on\n - 2024-08-06T13:58:24.773Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Human blood platelet Glycosylation Sites dataset contains glycosylation sites of thrombin-treated platelet proteins from Homo sapiens (taxid:9606). ESI-MS/MS and unbiased post-translational modification analysis of high-dose thrombin-treated releasate proteins, revealed O-glycosylation as a common modification of the secreted proteins and diverse O-glycan structures. A new form of domain-specific O-fucosylation was also detected within the elastin microfibril interface (EMI) domain of MMRN1, and was found to be important for it's secretion. The raw MS data can be found in the PRIDE repository under ID PXD045535.\n - The dataset was generated collaboratively by labs at several institutes: The Heart Research Institute, Central Clinical School, and Charles Perkins Centre, at the University of Sydney in Australia, the Department of Biochemistry and Molecular Biology at the University of Georgia in the USA, and the Institute for Glyco-Core Research at the Nagoya University in Japan.\n\nDescription Domain\n Keywords\n - o-glycosylation\n - o-fucosylation\n - o-mannosylation\n - o-linked\n - platelet\n - c-linked\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-Gluc modified residue against UniProtKB Canonical sequences.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-proteoform-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: human_proteoform_glycosylation_sites_platelet.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/compiled/human_proteoform_glycosylation_sites_platelet.csv\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_platelet.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/human_proteoform_glycosylation_sites_platelet.csv\n Name: human_proteoform_glycosylation_sites_platelet.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/human_proteoform_glycosylation_sites_platelet.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"5\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"11\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"2\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"7\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"1\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"1\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"1\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"site_type\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"11\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"11\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"composition\"\n Description: \"Composition of glycan\"\n Unique Values: \"7\"\n Name: \"peptide\"\n Description: \"Protein peptide\"\n Unique Values: \"12\"\n Name: \"peptide_start_pos\"\n Description: \"\"\n Unique Values: \"11\"\n Name: \"peptide_end_pos\"\n Description: \"\"\n Unique Values: \"11\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"notes\"\n Description: \"Notes\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.8.1/reviewed/human_proteoform_glycosylation_sites_platelet.csv" }