{ "bcoid": "GLY_000807", "title": "Yeast O-GlcNAc Glycosylation Sites (MCW)", "description": "The Yeast O-GlcNAc Glycosylation Sites (MCW) contains Saccharomyces cerevisiae S288C [taxid:559292] O-GlcNAc ...", "filename_list": "yeast_proteoform_glycosylation_sites_oglcnac_mcw.csv", "filename": "yeast_proteoform_glycosylation_sites_oglcnac_mcw.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Proteoform" ], "tag": [ "O-GlcNAc Glycosylation Sites (MCW)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "O14467-1...", "..." ], [ "P00815-1...", "..." ] ], "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": "uniprotkb_id" }, { "type": "string", "label": "entry_name" }, { "type": "string", "label": "organism" }, { "type": "string", "label": "full_name" }, { "type": "string", "label": "oglcnacscore" }, { "type": "string", "label": "oglcnac_sites" }, { "type": "string", "label": "phosphorylation_sites" }, { "type": "string", "label": "pmids" }, { "type": "string", "label": "sequence" }, { "type": "string", "label": "intracellular" }, { "type": "string", "label": "extracellular" }, { "type": "string", "label": "cytosol" }, { "type": "string", "label": "nucleus" }, { "type": "string", "label": "mitochndrion" }, { "type": "string", "label": "endoplasmic_reticulum" }, { "type": "string", "label": "golgi_apparatus" }, { "type": "string", "label": "plasma_membrane" }, { "type": "string", "label": "extracellular_region" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "carb_name" }, { "type": "string", "label": "glycosylation_subtype" }, { "type": "string", "label": "status" }, { "type": "string", "label": "uniprotkb_id" }, { "type": "string", "label": "gene_name" }, { "type": "string", "label": "recommended_name_full" }, { "type": "string", "label": "peptide" }, { "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" } ], [ "O14467-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "33229814", "protein_xref_oglcnac_db", "O14467", "O14467", "MBF1_YEAST", "Saccharomyces cerevisiae", "Multiprotein-bridging factor 1", "24.475439129846194", "", "S143", "33229814", "MSDWDTNTIIGSRARAGGSGPRANVARSQGQINAARRQGLVVSVDKKYGSTNTRGDNEGQRLTKVDRETDIVKPKKLDPNVGRAISRARTDKKMSQKDLATKINEKPTVVNDYEAARAIPNQQVLSKLERALGVKLRGNNIGSPLGAPKKK", "None", "None", "None", "None", "None", "None", "None", "None", "None", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "MBF1_YEAST", "MBF1", "Multiprotein-bridging factor 1", "", "", "", "", "", "" ], [ "P00815-1", "", "", "G49108TO", "O-linked", "protein_xref_pubmed", "33229814", "protein_xref_oglcnac_db", "P00815", "P00815", "HIS2_YEAST", "Saccharomyces cerevisiae", "Histidine biosynthesis trifunctional protein", "24.475439129846194", "", "", "33229814", "MVLPILPLIDDLASWNSKKEYVSLVGQVLLDGSSLSNEEILQFSKEEEVPLVALSLPSGKFSDDEIIAFLNNGVSSLFIASQDAKTAEHLVEQLNVPKERVVVEENGVFSNQFMVKQKFSQDKIVSIKKLSKDMLTKEVLGEVRTDRPDGLYTTLVVDQYERCLGLVYSSKKSIAKAIDLGRGVYYSRSRNEIWIKGETSGNGQKLLQISTDCDSDALKFIVEQENVGFCHLETMSCFGEFKHGLVGLESLLKQRLQDAPEESYTRRLFNDSALLDAKIKEEAEELTEAKGKKELSWEAADLFYFALAKLVANDVSLKDVENNLNMKHLKVTRRKGDAKPKFVGQPKAEEEKLTGPIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKLGLIPKDFQ", "None", "None", "None", "None", "None", "None", "None", "None", "None", "ECO_0000269", "GlcNac", "O-GlcNAcylation", "reviewed", "HIS2_YEAST", "HIS4", "Histidine biosynthesis trifunctional protein", "", "", "", "", "", "" ] ] }, "readme": "Name\n - Yeast O-GlcNAc Glycosylation Sites (MCW)\n\nVersion\n - v-2.10.1\n\nCreated on\n - 2022-08-16T20:56:25.251283\n\nModified on\n - 2025-03-04T16:50:33.173Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@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 - Stephanie Olivier-Van Stichelen [solivier@mcw.edu], Eugenia Wulff-Fuentes [ewulff@mcw.edu], Rex R. Berendt [rberendt@mcw.edu], Logan Massman [lmassman@mcw.edu], Laura Danner [ldanner@mcw.edu]\n\nChecksum\n - \n\nUsability Domain\n - The Yeast O-GlcNAc Glycosylation Sites (MCW) contains Saccharomyces cerevisiae S288C [taxid:559292] O-GlcNAc modifications on Serine and Threonine extracted from the publication and mapped to the UniProtKB canonical accession and fasta sequence. The GlyTouCan ID for the O-GlcNAc is G49108TO. The dataset also contains other information such as O-GlcNAc score, the count and the techniques used to determine the O-GlcNAc modification and the peptide sequence from the -5 to +5 postion of the modified residue. The dataset also containes disclaimer and notes where the position of sites in publication and in the fasta sequence varies.\n - The dataset is contributed from The O-GlcNAc Database maintained by Stephanie Olivier's lab \n - Wulff-Fuentes E, Berendt RR, Massman L, Danner L, Malard F, Vora J, Kahsay R, and Olivier-Van Stichelen S, The Yeast O-GlcNAcome Database and Meta-Analysis. Scientific Data 8, 25 (2021) \n - QC check - The python script is used to process each protein entry of the database table and perform quality control (QC). In the QC checks, the reported UniProtKB accessions in the database are matched with the GlyGen\u2019s yeast protein masterlist of UniProtKB canonical accessions to ensure all of the proteins belong to yeast species. Next, the O-GlcNAc site data that contained the amino acid residue and its position are mapped to the GlyGen\u2019s fasta sequence for the corresponding yeast UniProtKB canonical proteins. The amino acid residues and positions that don't match with the fasta sequence of the canonical protein were flagged and excluded from the table. Similarly, the protein entries that don't have any site information are also excluded. The entries that passed all the quality control steps are exported as a final csv dataset file whereas the excluded entries are exported in a log file with the reasons for exclusion for further manual verification.\n - DISCLAIMER - For each entry, an O-GlcNAc score was attributed to each O-GlcNAcylated protein, reflecting the confidence in the protein\u2019s O-GlcNAcylation identification. The score combined the number of articles and techniques used and the availability of some O-GlcNAcylation sites. Interestingly, a O-GlcNAc score of 3 or under, means that (1) no sites were identified, (2) only one technique was used, and (3) 1-2 articles were associated with the entry. Often identified from large-scale proteomics studies, at least an extra-validation step would be highly recommended to confirm their O-GlcNAcylation.\n\nDescription Domain\n Keywords\n - O-GlcNAc\n\n Pipeline Steps\n - Step-1: The script maps the UniProtKB accesions to the UniProtKB Canonical accessions and also checks the position and amino acid of O-GlcNAc modified residue against UniProtKB Canonical sequences. The script that processes this dataset matches the amino acid and position with the latest release fasta file as a QC check to eliminate the incorrect entries. The script also adds the -5 and +5 amino acids from the modified residue in the peptide field.\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: all_blacklisted_pmids.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/compiled/all_blacklisted_pmids.csv\n Name: yeast_protein_info_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/yeast_protein_info_uniprotkb.csv\n Name: yeast_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/yeast_protein_masterlist.csv\n Name: yeast_protein_recnames.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/yeast_protein_recnames.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2025_09_18/cellosaurus.txt\n Name: yeast_o_glcnacome_mcw.csv\n URI: https:/data.glygen.org/ln2downloads/mcw_oglcnac/2025_09_18/yeast_o_glcnacome_mcw.csv\n Output Subdomain\n Name: yeast_proteoform_glycosylation_sites_oglcnac_mcw.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/yeast_proteoform_glycosylation_sites_oglcnac_mcw.csv\n Name: yeast_proteoform_glycosylation_sites_oglcnac_mcw.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/yeast_proteoform_glycosylation_sites_oglcnac_mcw.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"463\"\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: \"1\"\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: \"2\"\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: \"463\"\n Name: \"uniprotkb_id\"\n Description: \"The entry name or mnemonic identifier assigned to the protein accession that consists of up to 11 uppercase alphanumeric characters for UniProtKB/Swiss-Prot entry and up to 16 uppercase alphanumeric characters for UniProtKB/TrEMBL entry with a defined naming convention\"\n Unique Values: \"926\"\n Name: \"entry_name\"\n Description: \"\"\n Unique Values: \"463\"\n Name: \"organism\"\n Description: \"Name of the species\"\n Unique Values: \"1\"\n Name: \"full_name\"\n Description: \"\"\n Unique Values: \"463\"\n Name: \"oglcnacscore\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"oglcnac_sites\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"phosphorylation_sites\"\n Description: \"\"\n Unique Values: \"325\"\n Name: \"pmids\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"sequence\"\n Description: \"Sequence\"\n Unique Values: \"463\"\n Name: \"intracellular\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"extracellular\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"cytosol\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"nucleus\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"mitochndrion\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"endoplasmic_reticulum\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"golgi_apparatus\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"plasma_membrane\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"extracellular_region\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"1\"\n Name: \"carb_name\"\n Description: \"carbohydrate name\"\n Unique Values: \"1\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\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_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: \"440\"\n Name: \"recommended_name_full\"\n Description: \"Recommended full name of the protein in the UniProtKB database\"\n Unique Values: \"463\"\n Name: \"peptide\"\n Description: \"Protein peptide\"\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: \"site_seq\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/yeast_proteoform_glycosylation_sites_oglcnac_mcw.csv" }