{ "bcoid": "GLY_000961", "title": "Human Glycosylation Sites ccRCC (PDC)", "description": "The Human Glycosylation Sites (PDC) dataset contains glycosylation information and intact glycopeptide ...", "filename_list": "human_proteoform_glycosylation_sites_pdc_ccrcc.csv", "filename": "human_proteoform_glycosylation_sites_pdc_ccrcc.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Proteoform" ], "tag": [ "Glycosylation Sites ccRCC (PDC)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P02751-15...", "542..." ], [ "P02751-15...", "542..." ] ], "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": "composition" }, { "type": "string", "label": "abundance" }, { "type": "string", "label": "source_tissue_id" }, { "type": "string", "label": "source_tissue_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": "site_type" }, { "type": "string", "label": "sequon" }, { "type": "string", "label": "sequon_type" }, { "type": "string", "label": "biospecimen_id" }, { "type": "string", "label": "isoform_mapping_notes" } ], [ "P02751-15", "542", "Asn", "G27058EU", "N-linked", "protein_xref_pubmed", "37074911", "protein_xref_pdc", "PDC000471", "N4H5F1S1G0", "14.12863483", "UBERON:0002113", "kidney", "542", "542", "Asn", "Asn", "HEEGHMLnCTCFGQGR", "known_site", "NCT", "NXT", "CPT0079430001", "" ], [ "P02751-15", "542", "Asn", "G27058EU", "N-linked", "protein_xref_pubmed", "37074911", "protein_xref_pdc", "PDC000471", "N4H5F1S1G0", "14.08341759", "UBERON:0002113", "kidney", "542", "542", "Asn", "Asn", "HEEGHMLnCTCFGQGR", "known_site", "NCT", "NXT", "CPT0023360001", "" ] ] }, "readme": "Name\n - Human Glycosylation Sites ccRCC (PDC)\n\nVersion\n - v-2.10.1\n\nCreated on\n - 2024-07-23T00:39:27\n\nModified on\n - 2024-07-23T00:40:06.813Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Jingyue Wu [jingyue.wu@email.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 Glycosylation Sites (PDC) dataset contains glycosylation information and intact glycopeptide abundances from Homo sapiens (taxid:9606) clear cell renal cell carcinoma (ccRCC) tumor and normal adjacent tissues collected by the CPTAC program. The processed data was retrieved from the Proteomic Data Commons (PDC) and can be accessed at https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471. GlyTouCan and UniProtKB accessions were mapped by the GlyGen team to the glycan compositions and gene names provided by the authors, respectively. If you use this dataset please provide proper attribution to the source publication[1], PDC and GlyGen.\n - References: 1) Lih TM, Cho KC, Schnaubelt M, Hu Y, Zhang H. Integrated glycoproteomic characterization of clear cell renal cell carcinoma. Cell Rep. 2023 May 30;42(5):112409. doi: 10.1016/j.celrep.2023.112409. Epub 2023 Apr 18. PMID: 37074911; PMCID: PMC10247542.\n\nDescription Domain\n Keywords\n - N-linked glycosylation\n - glycoproteomics\n - clear cell renal cell carcinoma\n - PDC\n\n Pipeline Steps\n - Step-1: The script performs QC steps and creates a proteoform dataset according to the GlyGen data model.\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_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_protein_masterlist.csv\n Name: pdc_glytoucan_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/misc/pdc_glytoucan_mapping.csv\n Name: toy.tsv\n URI: https:/data.glygen.org/ln2downloads/pdc/2024_04_18/toy.tsv\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_pdc_ccrcc.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_proteoform_glycosylation_sites_pdc_ccrcc.csv\n Name: human_proteoform_glycosylation_sites_pdc_ccrcc.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/human_proteoform_glycosylation_sites_pdc_ccrcc.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1079\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"977\"\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: \"230\"\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: \"composition\"\n Description: \"Composition of glycan\"\n Unique Values: \"230\"\n Name: \"abundance\"\n Description: \" Abundance ratio of the glycan.\"\n Unique Values: \"823696\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"1\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"974\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"974\"\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: \"2461\"\n Name: \"site_type\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"sequon\"\n Description: \"\"\n Unique Values: \"53\"\n Name: \"sequon_type\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"biospecimen_id\"\n Description: \"\"\n Unique Values: \"194\"\n Name: \"isoform_mapping_notes\"\n Description: \"\"\n Unique Values: \"16\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/human_proteoform_glycosylation_sites_pdc_ccrcc.csv" }