{ "bcoid": "GLY_000888", "title": "Human Glycosylation Sites (EMBL)", "description": "The Human Glycosylation Sites (EMBL) dataset contains glycosylation information (mainly for N-glycosylation) ...", "filename_list": "human_proteoform_glycosylation_sites_embl.csv", "filename": "human_proteoform_glycosylation_sites_embl.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Proteoform" ], "tag": [ "Glycosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q5JTV8-1...", "399..." ], [ "Q13563-1...", "305..." ] ], "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": "source_tissue_id" }, { "type": "string", "label": "source_tissue_name" }, { "type": "string", "label": "source_cell_line_cellosaurus_id" }, { "type": "string", "label": "source_cell_line_cellosaurus_name" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "start_aa" }, { "type": "string", "label": "end_aa" }, { "type": "string", "label": "site_seq" }, { "type": "string", "label": "source_glycan_type" }, { "type": "string", "label": "source_gene_name" }, { "type": "string", "label": "composition" }, { "type": "string", "label": "composition_mass" }, { "type": "string", "label": "n_sequon" }, { "type": "string", "label": "n_sequon_type" }, { "type": "string", "label": "isoform_mapping_notes" } ], [ "Q5JTV8-1", "399", "Asn", "G62765YT", "N-linked", "protein_xref_doi", "10.1101/2023.09.13.557529", "protein_xref_data_submission", "GLY_000888", "UBERON:0002113", "kidney", "CVCL_0063", "HEK293T", "399", "399", "Asn", "Asn", "HLNSSHPR", "high mannose", "TOR1AIP1", "HexNAc(2)Hex(8)", "1702.5814", "NSS", "NXS", "" ], [ "Q13563-1", "305", "Asn", "G63332OE", "N-linked", "protein_xref_doi", "10.1101/2023.09.13.557529", "protein_xref_data_submission", "GLY_000888", "UBERON:0002113", "kidney", "CVCL_0063", "HEK293T", "305", "305", "Asn", "Asn", "MQPSNQTEADNR", "sialylated", "PKD2", "HexNAc(6)Hex(8)NeuAc(2)", "3097.0898", "NRS", "NXS", "" ] ] }, "readme": "Name\n - Human Glycosylation Sites (EMBL)\n\nVersion\n - v-2.10.1\n\nModified on\n - 2024-05-21T13:23:51.724Z\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 - Clement Potel [clement.potel@embl.de], Mira Burtscher [mira.burtscher@embl.de], Martin Garrido [martin.garrido@embl.de]\n\nChecksum\n - \n\nUsability Domain\n - The Human Glycosylation Sites (EMBL) dataset contains glycosylation information (mainly for N-glycosylation) on Homo sapiens (taxid:9606) cell line (HelaK and HEK293T) proteins. The data is submitted by Dr. Clement Potel, Dr. Mira Burtscher and Dr. Martin Garrido, of the Genome Biology Unit, EMBL based on the publication 'Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome.' GlyTouCan accessions were mapped by the GlyGen team to the glycan compositions provided by the authors. If you use this dataset please provide proper attribution to the data source [1], EMBL and GlyGen.\n - References: 1) Potel C, Burtscher ML, Garrido-Rodriguez M, Brauer-Nikonow A, Becher I, Typas A, Zimmermann M, Savitski M. Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome. bioRxiv 2023.09.13.557529; doi:10.1101/2023.09.13.557529.\n\nDescription Domain\n\n Pipeline Steps\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: n_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/misc/n_sequon_info.csv\n Name: glygen_upload.csv\n URI: https:/data.glygen.org/ln2downloads/embl/2024_02_09/glygen_upload.csv\n Name: names.tsv\n URI: https:/data.glygen.org/ln2downloads/glytoucan/2025_10_09/export/names.tsv\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_embl.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_proteoform_glycosylation_sites_embl.csv\n Name: human_proteoform_glycosylation_sites_embl.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_proteoform_glycosylation_sites_embl.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"2751\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"1562\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"1\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"541\"\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: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"2\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"2\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"2\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"1563\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1563\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"5443\"\n Name: \"source_glycan_type\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"source_gene_name\"\n Description: \"\"\n Unique Values: \"2757\"\n Name: \"composition\"\n Description: \"Composition of glycan\"\n Unique Values: \"541\"\n Name: \"composition_mass\"\n Description: \"Mass of the glycan\"\n Unique Values: \"539\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"69\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"isoform_mapping_notes\"\n Description: \"\"\n Unique Values: \"25\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/human_proteoform_glycosylation_sites_embl.csv" }