{ "bcoid": "GLY_000624", "title": "Mouse Glycogenes", "description": "This mouse glycogenes dataset is retrieved from stem cell analysis which was done with qRT-PCR analysis ...", "filename": "mouse_protein_glycogenes.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Protein", "tags": "Glycogenes", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q64676-1...", "22239..." ], [ "Q63886-1...", "394436..." ] ], "headers": [ "uniprotkb_ca...", "gene_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "gene_id" }, { "type": "string", "label": "gene_name" }, { "type": "string", "label": "gene_names_alternative" }, { "type": "string", "label": "uniprotkb_protein_recommended_name" }, { "type": "string", "label": "glycoenzyme_gene_id" }, { "type": "string", "label": "gene_group" } ], [ "Q64676-1", "22239", "Ugt8", "Cgt;Ugt4;Ugt8a", "2-hydroxyacylsphingosine 1-beta-galactosyltransferase", "GT01_M03", "Glycosyltransferase" ], [ "Q63886-1", "394436", "Ugt1a1", "Ugt1", "UDP-glucuronosyltransferase 1A1", "GT01_M07", "Glycosyltransferase" ], [ "Q80X89-1", "94215", "Ugt2a1", "", "UDP-glucuronosyltransferase 2A1", "GT01_M08", "Glycosyltransferase" ], [ "Q8R084-1", "71773", "Ugt2b1", "", "UDP-glucuronosyltransferase", "GT01_M10", "Glycosyltransferase" ], [ "Q8K154-1", "100727", "Ugt2b34", "AI788959", "UDP-glucuronosyltransferase", "GT01_M11", "Glycosyltransferase" ], [ "Q8VCN3-1", "112417", "Ugt2b37", "", "UDP-glucuronosyltransferase", "GT01_M12", "Glycosyltransferase" ], [ "Q9D081-1", "66789", "Alg14", "", "UDP-N-acetylglucosamine transferase subunit ALG14 homolog", "GT01_M15", "Glycosyltransferase" ], [ "Q6ZQM8-1", "394432", "Ugt1a7", "Ugt1a7c", "UDP-glucuronosyltransferase 1A7", "GT01_M16", "Glycosyltransferase" ], [ "Q8BJL9-1", "243085", "Ugt2b35", "", "UDP-glucuronosyltransferase", "GT01_M20", "Glycosyltransferase" ], [ "Q8BML3-1", "320302", "Glt28d2", "", "N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase", "GT01_M21", "Glycosyltransferase" ], [ "Q9D8C3-1", "67574", "Alg13", "Glt28d1", "Putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13", "GT01_M22", "Glycosyltransferase" ], [ "Q6PDD0-1", "552899", "Ugt2a2", "", "UDP-glucuronosyltransferase 2A2", "GT01_M23", "Glycosyltransferase" ], [ "Q3UEP4-1", "231396", "Ugt2b36", "", "UDP-glucuronosyltransferase", "GT01_M24", "Glycosyltransferase" ], [ "Q9DB25-1", "66248", "Alg5", "", "Dolichyl-phosphate beta-glucosyltransferase", "GT02_M01", "Glycosyltransferase" ], [ "Q3U129-1", "210004", "B3gntl1", "", "UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like protein 1", "GT02_M02", "Glycosyltransferase" ], [ "O70152-1", "13480", "Dpm1", "", "Dolichol-phosphate mannosyltransferase subunit 1", "GT02_M03", "Glycosyltransferase" ], [ "Q61647-1", "15116", "Has1", "Has", "Hyaluronan synthase 1", "GT02_M04", "Glycosyltransferase" ], [ "P70312-1", "15117", "Has2", "", "Hyaluronan synthase 2", "GT02_M05", "Glycosyltransferase" ], [ "O08650-1", "15118", "Has3", "", "Hyaluronan synthase 3", "GT02_M06", "Glycosyltransferase" ], [ "Q9Z1E4-1", "14936", "Gys1", "Gys;Gys3", "Glycogen [starch] synthase, muscle", "GT03_M01", "Glycosyltransferase" ], [ "Q8VCB3-1", "232493", "Gys2", "", "Glycogen [starch] synthase, liver", "GT03_M02", "Glycosyltransferase" ], [ "Q9DBE8-1", "56737", "Alg2", "", "Alpha-1,3/1,6-mannosyltransferase ALG2", "GT04_M01", "Glycosyltransferase" ], [ "Q3TZM9-1", "207958", "Alg11", "", "GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase", "GT04_M02", "Glycosyltransferase" ], [ "Q64323-1", "18700", "Piga", "", "Phosphatidylinositol N-acetylglucosaminyltransferase subunit A", "GT04_M03", "Glycosyltransferase" ], [ "Q8BW56-1", "227835", "Gtdc1", "", "Glycosyltransferase-like domain-containing protein 1", "GT04_M04", "Glycosyltransferase" ], [ "A4FUP9-1", "319804", "Glt1d1", "", "Glycosyltransferase 1 domain-containing protein 1", "GT04_M05", "" ], [ "P23336-1", "14594", "Ggta1", "Ggta-1", "N-acetyllactosaminide alpha-1,3-galactosyltransferase", "GT06_M01", "Glycosyltransferase" ], [ "P38649-1", "80908", "Abo", "", "Histo-blood group ABO system transferase", "GT06_M02", "Glycosyltransferase" ], [ "Q8VI38-1", "227671", "Gbgt1", "Fgs", "Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1", "GT06_M03", "Glycosyltransferase" ], [ "A2AUQ7-1", "75859", "Ggta1l1", "", "N-acetyllactosaminide alpha-1,3-galactosyltransferase-like 1", "GT06_M04", "Glycosyltransferase" ], [ "Q3V1N9-1", "215493", "A3galt2", "Igb3s", "Alpha-1,3-galactosyltransferase 2", "GT06_M05", "Glycosyltransferase" ], [ "Q2NKH9-1", "71103", "Glt6d1", "", "Glycosyltransferase 6 domain-containing protein 1", "GT06_M06", "Glycosyltransferase" ], [ "Q8BJQ9-1", "234356", "Csgalnact1", "Chgn;Galnact1", "Chondroitin sulfate N-acetylgalactosaminyltransferase 1", "GT07_M01", "Glycosyltransferase" ], [ "P15535-1", "14595", "B4galt1", "Ggtb;Ggtb2", "Beta-1,4-galactosyltransferase 1", "GT07_M02", "Glycosyltransferase" ], [ "Q9Z2Y2-1", "53418", "B4galt2", "", "Beta-1,4-galactosyltransferase 2", "GT07_M03", "Glycosyltransferase" ], [ "Q91YY2-1", "57370", "B4galt3", "", "Beta-1,4-galactosyltransferase 3", "GT07_M04", "Glycosyltransferase" ], [ "Q9JJ04-1", "56375", "B4galt4", "", "Beta-1,4-galactosyltransferase 4", "GT07_M05", "Glycosyltransferase" ], [ "Q9JMK0-1", "56336", "B4galt5", "Bgt-5", "Beta-1,4-galactosyltransferase 5", "GT07_M06", "Glycosyltransferase" ], [ "Q9WVK5-1", "56386", "B4galt6", "", "Beta-1,4-galactosyltransferase 6", "GT07_M07", "Glycosyltransferase" ], [ "Q8R087-1", "218271", "B4galt7", "Xgalt1", "Beta-1,4-galactosyltransferase 7", "GT07_M08", "Glycosyltransferase" ], [ "Q766D5-1", "330671", "B4galnt4", "", "N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase 1", "GT07_M09", "Glycosyltransferase" ], [ "Q6L8S8-1", "330406", "B4galnt3", "", "Beta-1,4-N-acetylgalactosaminyltransferase 3", "GT07_M10", "Glycosyltransferase" ], [ "Q6ZQ11-1", "269941", "Chsy1", "Kiaa0990", "Chondroitin sulfate synthase 1", "GT07_M11", "Glycosyltransferase" ], [ "Q6IQX7-1", "74241", "Chpf", "Css2;D1Bwg1363e", "Chondroitin sulfate synthase 2", "GT07_M12", "Glycosyltransferase" ], [ "Q8C1F4-1", "78752", "Csgalnact2", "Chgn2;Galnact2", "Chondroitin sulfate N-acetylgalactosaminyltransferase 2", "GT07_M13", "Glycosyltransferase" ], [ "Q3UU43-1", "100910", "Chpf2", "", "Hexosyltransferase", "GT07_M14", "Glycosyltransferase" ], [ "Q5DTK1-1", "78923", "Chsy3", "Chsy2;Css3;Kiaa4168", "Chondroitin sulfate synthase 3", "GT07_M15", "Glycosyltransferase" ], [ "Q6NSU3-1", "76485", "Glt8d1", "", "Glycosyltransferase 8 domain-containing protein 1", "GT08_M01", "Glycosyltransferase" ], [ "Q9R062-1", "27357", "Gyg", "Gyg1", "Glycogenin-1", "GT08_M02", "Glycosyltransferase" ], [ "Q3U4G3-1", "268880", "Xxylt1", "", "Xyloside xylosyltransferase 1", "GT08_M03", "Glycosyltransferase" ], [ "Q9Z1M7-1", "16795", "Large1", "Large;Kiaa0609", "LARGE xylosyl- and glucuronyltransferase 1", "GT08_M04", "Glycosyltransferase" ], [ "Q640P4-1", "74782", "Glt8d2", "", "Glycosyltransferase 8 domain-containing protein 2", "GT08_M05", "Glycosyltransferase" ], [ "Q5XPT3-1", "228366", "Large2", "Gyltl1b", "LARGE xylosyl- and glucuronyltransferase 2", "GT08_M06", "Glycosyltransferase" ], [ "Q810K9-1", "232313", "Gxylt2", "Glt8d4", "Glucoside xylosyltransferase 2", "GT08_M07", "Glycosyltransferase" ], [ "Q3UHH8-1", "223827", "Gxylt1", "Glt8d3;Gm87", "Glucoside xylosyltransferase 1", "GT08_M08", "Glycosyltransferase" ], [ "Q8BHC9-1", "73068", "Fut11", "", "Alpha-(1,3)-fucosyltransferase 11", "GT10_M01", "Glycosyltransferase" ], [ "Q11127-1", "14345", "Fut4", "Elft", "Alpha-(1,3)-fucosyltransferase 4", "GT10_M02", "Glycosyltransferase" ], [ "Q11131-1", "14347", "Fut7", "", "Alpha-(1,3)-fucosyltransferase 7", "GT10_M03", "Glycosyltransferase" ], [ "O88819-1", "14348", "Fut9", "", "4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9", "GT10_M04", "Glycosyltransferase" ], [ "Q5F2L2-1", "171167", "Fut10", "", "Alpha-(1,3)-fucosyltransferase 10", "GT10_M05", "Glycosyltransferase" ], [ "O09160-1", "14343", "Fut1", "", "Galactoside alpha-(1,2)-fucosyltransferase 1", "GT11_M01", "Glycosyltransferase" ], [ "Q9JL27-1", "14344", "Fut2", "Sec2", "Galactoside alpha-(1,2)-fucosyltransferase 2", "GT11_M02", "Glycosyltransferase" ], [ "P97353-1", "56546", "Sec1", "Fut3", "Galactoside 2-alpha-L-fucosyltransferase Sec1", "GT11_M03", "Glycosyltransferase" ], [ "Q09199-1", "14422", "B4galnt2", "Galgt2;Ggm3", "Beta-1,4 N-acetylgalactosaminyltransferase 2", "GT12_M01", "Glycosyltransferase" ], [ "Q09200-1", "14421", "B4galnt1", "Galgt;Galgt1;Ggm2", "Beta-1,4 N-acetylgalactosaminyltransferase 1", "GT12_M02", "Glycosyltransferase" ], [ "P27808-1", "17308", "Mgat1", "Gnt1", "Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase", "GT13_M01", "Glycosyltransferase" ], [ "Q91X88-1", "68273", "Pomgnt1", "", "Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1", "GT13_M02", "Glycosyltransferase" ], [ "P97402-1", "14538", "Gcnt2", "Ignt3;Ignt1", "N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase", "GT14_M01", "Glycosyltransferase" ], [ "Q09324-1", "14537", "Gcnt1", "", "Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase", "GT14_M02", "Glycosyltransferase" ], [ "Q5JCT0-1", "72077", "Gcnt3", "", "Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 3", "GT14_M03", "Glycosyltransferase" ], [ "Q9EPL0-1", "217119", "Xylt2", "", "Xylosyltransferase 2", "GT14_M04", "Glycosyltransferase" ], [ "Q811B1-1", "233781", "Xylt1", "", "Xylosyltransferase 1", "GT14_M05", "Glycosyltransferase" ], [ "Q3V3K7-1", "654821", "Gcnt7", "", "Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 7", "GT14_M06", "Glycosyltransferase" ], [ "Q99K95-1", "66404", "Rtf2", "Rtfdc1", "Replication termination factor 2", "GT14_M07", "Glycosyltransferase" ], [ "E9Q649-1", "218476", "Gcnt4", "", "Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4", "GT14_M09", "Glycosyltransferase" ], [ "Q921V5-1", "217664", "Mgat2", "", "Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase", "GT16_M01", "Glycosyltransferase" ], [ "Q10470-1", "17309", "Mgat3", "", "Beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase", "GT17_M01", "Glycosyltransferase" ], [ "Q765H6-1", "268510", "Mgat5b", "", "Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B", "GT18_M01", "Glycosyltransferase" ], [ "Q765H6-1", "268510", "Mgat5b", "", "Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B", "GT18_M01b", "Glycosyltransferase" ], [ "Q8R4G6-1", "107895", "Mgat5", "", "Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A", "GT18_M02", "Glycosyltransferase" ], [ "O88693-1", "22234", "Ugcg", "", "Ceramide glucosyltransferase", "GT21_M01", "Glycosyltransferase" ], [ "Q8VDB2-1", "223774", "Alg12", "", "Dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase", "GT22_M01", "Glycosyltransferase" ], [ "Q8VDI9-1", "102580", "Alg9", "", "Alpha-1,2-mannosyltransferase ALG9", "GT22_M02", "Glycosyltransferase" ], [ "Q9JJQ0-1", "55981", "Pigb", "Ccpg1", "GPI mannosyltransferase 3", "GT22_M03", "Glycosyltransferase" ] ] }, "readme": "Name\n - Mouse Glycogenes\n\nVersion\n - 1.11.2\n\nCreated on\n - 2022-03-29T10:34:01.428342\n\nModified on\n - 2022-03-30T11:48:46.807300\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - This mouse glycogenes dataset is retrieved from stem cell analysis which was done with qRT-PCR analysis [PMID:18411279]. It contains a list of UniProtKB accessions full and shortened mouse[taxonomy:10090] protein names mapped to NCBI gene and MGI IDs. The GT, GH, CBM and CE groups are defined by CAZy families. Following those groups are Lectins (following Kurt Drickamer\u2019s groupings), then several other glycan-related genes like GL (Glycolipid-related), GR (GAG-related), etc. If you use this dataset, please provide proper attribution to RefSeq, EMBL-EBI-UniProtKB and GlyGen. Cite:PMID:26553804, PMID:33237286 and PMID:31616925. The dataset can be used for obtaining UniProtKB recommended names (full and short) and HGNC gene names for UniProtKB canonical proteins. If you use this dataset, please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. This dataset can be used for obtaining proteins grouped as they are defined by CAZy. \n\nDescription Domain\n Keywords\n - glycogenes\n\n Pipeline Steps\n - Step-1: The script maps the gene ids and gene names from the source file to UniProtKB canonical accession and then then adds the protein recommneded name and alternative gene names. The script extracts gene identifier and group fields as is from the source input file. The script filters entries that are not mapped in the log file.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: mouse_protein_xref_geneid.csv\n URI: https:/data.glygen.org/ln2releases/data/v-1.12.3/reviewed/mouse_protein_xref_geneid.csv\n Name: mouse_glycogenes.csv\n URI: https:/data.glygen.org/ln2downloads/glycogenes/2022_02_16/mouse_glycogenes.csv\n Output Subdomain\n Name: mouse_protein_glycogenes.csv\n URI: https:/data.glygen.org/ln2releases/data/v-1.12.3/reviewed/mouse_protein_glycogenes.csv\n Name: mouse_protein_glycogenes.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-1.12.3/reviewed/mouse_protein_glycogenes.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"891\"\n Name: \"gene_id\"\n Description: \"NCBI Gene identifier\"\n Unique Values: \"874\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"891\"\n Name: \"gene_names_alternative\"\n Description: \"\"\n Unique Values: \"492\"\n Name: \"uniprotkb_protein_recommended_name\"\n Description: \"The recommended full name of the protein in UniProtKB\"\n Unique Values: \"854\"\n Name: \"glycoenzyme_gene_id\"\n Description: \"\"\n Unique Values: \"916\"\n Name: \"gene_group\"\n Description: \"\"\n Unique Values: \"58\"", "downloadurl": "/ln2data/releases/data/v-1.12.3/reviewed/mouse_protein_glycogenes.csv" }