{ "bcoid": "GLY_001372", "title": "Hamster Glycosyltransferases", "description": "The Hamster Glycosyltransferases dataset contains list of Cricetulus griseus [taxid:10029] glycosyltransferases ...", "filename_list": "hamster_protein_glycosyltransferase.csv", "filename": "hamster_protein_glycosyltransferase.csv", "filetype": "csv", "categories": { "species": [ "Cricetulus griseus" ], "molecule": [ "Protein" ], "tag": [ "Glycosyltransferases" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P24140-1...", "Cricetulus g..." ], [ "P83337-1...", "Cricetulus g..." ] ], "headers": [ "uniprotkb_ca...", "species..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "species" }, { "type": "string", "label": "status" }, { "type": "string", "label": "gene_symbol" }, { "type": "string", "label": "uniprotkb_protein_name" }, { "type": "string", "label": "ec_number" }, { "type": "string", "label": "brenda_ec_number" }, { "type": "string", "label": "cazy_gt_family" }, { "type": "string", "label": "interpro_id" }, { "type": "string", "label": "pfam_ac" }, { "type": "string", "label": "go_molecular_function" } ], [ "P24140-1", "Cricetulus griseus (Chinese hamster) (Cricetulus barabensis griseus)", "reviewed", "DPAGT1", "UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.15) (GlcNAc-1-P transferase) (G1PT) (GPT) (N-acetylglucosamine-1-phosphate transferase)", "2.7.8.15", "", "", "IPR048439|IPR000715|IPR033895", "PF21383|PF00953", "glycosyltransferase activity [GO:0016757]| identical protein binding [GO:0042802]| metal ion binding [GO:0046872]| UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity [GO:0003975]| UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity [GO:0003976]" ], [ "P83337-1", "Cricetulus griseus (Chinese hamster) (Cricetulus barabensis griseus)", "reviewed", "POFUT1", "GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221) (Peptide-O-fucosyltransferase 1) (O-FucT-1)", "2.4.1.221", "", "", "IPR019378|IPR039922", "PF10250", "glycosyltransferase activity [GO:0016757]| peptide-O-fucosyltransferase activity [GO:0046922]| transferase activity [GO:0016740]" ] ] }, "readme": "Name\n - Hamster Glycosyltransferases\n\nVersion\n - v-2.8.1\n\nCreated on\n - \n\nModified on\n - \n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@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 - Jeet Vora [jeetvora@gwu.edu], Hayley Dingerdissen [hmhamilt@gwmail.gwu.edu]\n\nChecksum\n - \n\nUsability Domain\n - The Hamster Glycosyltransferases dataset contains list of Cricetulus griseus [taxid:10029] glycosyltransferases enzymes with evidence of glycosyltransferase activity defined by one or several of the following criteria: gene ontology (GO) or UniProtKB/Swiss-Prot annotation; classification by CAZY database; inclusion in the GT panel developed by the Consortium of Functional Glycomics (CFG); domains reported by InterPro and Pfam. The dataset was created by: Proteomes, gene and protein lists were retrieved from UniProtKB/Swiss-Prot. The full set of proteins comprising the hamster proteome was retrieved with the following search terms: keyword:\"Complete proteome [KW-0181]\" (now removed from UniProtKB) AND reviewed:yes AND organism:\"Cricetulus griseus (Chinese hamster) [10029]\". To retrieve the list of all hamster glycosyltransferases, the full list of hamster proteins were filtered using Gene Ontology (GO) terms, with molecular function GO term, GO:0016757 transferase activity, transferring glycosyl groups, each corresponding to a unique gene. To ensure the gene list was comprehensive with respect to available annotations, entries were cross-referenced with two external glycomics databases: the Carbohydrate Active Enzymes database (CAZY, http://www.cazy.org/), the Consortium for Functional Glycomics (CFG) functional glycomics gateway (http://www.functionalglycomics.org/), BRENDA (https://www.brenda-enzymes.org/index.php) and Enzyme Portal (https://www.ebi.ac.uk/enzymeportal/). The list was then filtered to remove any duplicate references resulting from cross-database redundancy or secondary accessions. Entries not already contained in the GO-derived glycosyltransferase gene list were added to the list. InterPro and Pfam accessions were then retrieved for all genes currently in the list. For GlyGen, GTs that were not part of glycan metabolism were removed to produce a manually curated list of glycosyltransferase. If you use this dataset please provide proper attribution to UniProtKB and GlyGen.\n\nDescription Domain\n Keywords\n - GT\n - glycosyltransferase\n - CAZy\n - CFG\n - EC Number\n - GO\n\n Pipeline Steps\n - Step-1: The script maps and replaces the UniProtKb accession to the UniProtKB canonical accession\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-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: hamster_protein_glycosyltransferase.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/compiled/hamster_protein_glycosyltransferase.csv\n Name: hamster_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/hamster_protein_masterlist.csv\n Output Subdomain\n Name: hamster_protein_glycosyltransferase.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/hamster_protein_glycosyltransferase.csv\n Name: hamster_protein_glycosyltransferase.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/hamster_protein_glycosyltransferase.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"species\"\n Description: \"Species of the protein.\"\n Unique Values: \"1\"\n Name: \"status\"\n Description: \"Status of the protein record in UniProtKB database that can be reviewed for UniProtKB/Swiss-Prot entry or unreviewed for UniProtKB/TrEMBL entry\"\n Unique Values: \"1\"\n Name: \"gene_symbol\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC)\"\n Unique Values: \"3\"\n Name: \"uniprotkb_protein_name\"\n Description: \"Name of the protein in UniProtKB database\"\n Unique Values: \"3\"\n Name: \"ec_number\"\n Description: \"Enzyme Commision number assigned to an enzyme by Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB)\"\n Unique Values: \"3\"\n Name: \"brenda_ec_number\"\n Description: \"Enzyme Commission (EC) number assigned to enzyme in BRENDA database\"\n Unique Values: \"1\"\n Name: \"cazy_gt_family\"\n Description: \"The Family assigned to glycosyltransferase in the CAZy (Carbohydrate-Active enZYmes) database\"\n Unique Values: \"2\"\n Name: \"interpro_id\"\n Description: \"InterPro Identifier\"\n Unique Values: \"3\"\n Name: \"pfam_ac\"\n Description: \"Accession assigned to the protein family in the Pfam database\"\n Unique Values: \"3\"\n Name: \"go_molecular_function\"\n Description: \"\"The elemental activities of a gene product at the molecular level\"\n Unique Values: \"3\"", "downloadurl": "/ln2data/releases/data/v-2.8.1/reviewed/hamster_protein_glycosyltransferase.csv" }