{ "bcoid": "GLY_000960", "title": "Human Glycosylation Sites Diabetes Glycomics Study", "description": "The Human Glycosylation Sites Diabetes Glycomics Study dataset contains abundance information on the ...", "filename_list": "human_proteoform_glycosylation_sites_diabetes_glycomic.csv", "filename": "human_proteoform_glycosylation_sites_diabetes_glycomic.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Proteoform" ], "tag": [ "Diabetes glycomic study" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "...", "..." ], [ "...", "..." ] ], "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": "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": "sample_id" } ], [ "", "", "", "G59722IA", "N-linked", "protein_xref_pubmed", "28905229", "protein_xref_data_submission", "GLY_000960", "0.079695833", "UBERON:0001969", "blood plasma", "", "", "", "", "4002080252" ], [ "", "", "", "G62220SM", "N-linked", "protein_xref_pubmed", "28905229", "protein_xref_data_submission", "GLY_000960", "1.402411565", "UBERON:0001969", "blood plasma", "", "", "", "", "4002080252" ] ] }, "readme": "Name\n - Human Glycosylation Sites Diabetes Glycomics Study\n\nVersion\n - v-2.9.1\n\nModified on\n - 2024-06-04T13:24:39.398Z\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 - Olga Gornik [ogornik@pharma.hr], Nadja Rudman [najda.rudman@gmail.com]\n\nChecksum\n - \n\nUsability Domain\n - The Human Glycosylation Sites Diabetes Glycomics Study dataset contains abundance information on the plasma N-glycome of individuals participating in the FinRisk study. Baseline samples were analyzed from 37 individuals who developed type 2 diabetes within 10 years and 37 sex and age matched individuals who remained normoglycaemic. HILIC-UPLC chromatograms were separated into 46 peaks, and were assigned to the most abundant glycan structures in each peak (see Fig 1 of Ref. 1). The data is submitted by Dr. Olga Gornik, Faculty of Pharmacy and Biochemistry, University of Zagreb. GlyTouCan accessions were mapped to each peak by the GlyGen team based on the glycan topology. If you use this dataset please provide proper attribution to the source publication [1] and GlyGen.\n - References: 1) Keser T, Gornik I, Vu\u010dkovi\u0107 F, Selak N, Pavi\u0107 T, Luki\u0107 E, Gudelj I, Ga\u0161parovi\u0107 H, Bio\u010dina B, Tilin T, Wennerstr\u00f6m A, M\u00e4nnist\u00f6 S, Salomaa V, Havulinna A, Wang W, Wilson JF, Chaturvedi N, Perola M, Campbell H, Lauc G, Gornik O. Increased plasma N-glycome complexity is associated with higher risk of type 2 diabetes. Diabetologia. 2017;60(12):2352-2360. doi:10.1007/s00125-017-4426-9. PMID:28905229.\n\nDescription Domain\n Keywords\n - N-glycome\n - Publications\n - Citations\n - PubMed\n - Diabetes\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: fig_to_gtc.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/misc/fig_to_gtc.csv\n Name: HG_FinnRisk.txt\n URI: https:/data.glygen.org/ln2downloads/zagreb/2024_04_18/HG_FinnRisk.txt\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_diabetes_glycomic.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_proteoform_glycosylation_sites_diabetes_glycomic.csv\n Name: human_proteoform_glycosylation_sites_diabetes_glycomic.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_proteoform_glycosylation_sites_diabetes_glycomic.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"1\"\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: \"39\"\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: \"abundance\"\n Description: \" Abundance ratio of the glycan.\"\n Unique Values: \"3403\"\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: \"1\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"sample_id\"\n Description: \"\"\n Unique Values: \"74\"", "downloadurl": "/ln2data/releases/data/v-2.9.1/reviewed/human_proteoform_glycosylation_sites_diabetes_glycomic.csv" }