{ "bcoid": "GLY_000709", "title": "Mouse O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas)", "description": "The Mouse O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas) contains mouse (taxid:10090) O-GlcNAc modifications ...", "filename": "mouse_proteoform_glycosylation_sites_oglcnac_atlas.csv", "filetype": "csv", "categories": { "species": [ "Mus musculus" ], "molecule": [ "Proteoform" ], "tags": [ "O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas)" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "A0A0A6YVU8-1...", "211..." ], [ "A0A0A6YVU8-1...", "211..." ] ], "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": 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"synaptosomes", "", "", "ITEVT-T-MTSTV", "1717", "1717", "Thr", "Thr", "T" ], [ "A2A654-1", "1717", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "34678516", "protein_xref_oglcnac_db", "A2A654", "synaptosome", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "ITEVT-T-MTSTV", "1717", "1717", "Thr", "Thr", "T" ], [ "A2A654-1", "1717", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "ITEVT-T-MTSTV", "1717", "1717", "Thr", "Thr", "T" ], [ "A2A654-1", "1717", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "22645316", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "ITEVT-T-MTSTV", "1717", "1717", "Thr", "Thr", "T" ], [ "A2A654-1", "1719", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "EVTTM-T-STVAT", "1719", "1719", "Thr", "Thr", "T" ], [ "A2A654-1", "1719", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "22645316", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "EVTTM-T-STVAT", "1719", "1719", "Thr", "Thr", "T" ], [ "A2A654-1", "1742", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "KQTVV-S-STENC", "1742", "1742", "Ser", "Ser", "S" ], [ "A2A654-1", "1742", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "21606357", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "KQTVV-S-STENC", "1742", "1742", "Ser", "Ser", "S" ], [ "A2A654-1", "1743", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "QTVVS-S-TENCA", "1743", "1743", "Ser", "Ser", "S" ], [ "A2A654-1", "1743", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "21606357", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "QTVVS-S-TENCA", "1743", "1743", "Ser", "Ser", "S" ], [ "A2A654-1", "1750", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "ENCAR-S-TVTTT", "1750", "1750", "Ser", "Ser", "S" ], [ "A2A654-1", "1750", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "21606357", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "ENCAR-S-TVTTT", "1750", "1750", "Ser", "Ser", "S" ], [ "A2A654-1", "1750", "Ser", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "ENCAR-S-TVTTT", "1750", "1750", "Ser", "Ser", "S" ], [ "A2A654-1", "1750", "Ser", "G49108TO", "O-linked", "protein_xref_pubmed", "22645316", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "ENCAR-S-TVTTT", "1750", "1750", "Ser", "Ser", "S" ], [ "A2A654-1", "1751", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "NCARS-T-VTTTT", "1751", "1751", "Thr", "Thr", "T" ], [ "A2A654-1", "1751", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "21606357", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "NCARS-T-VTTTT", "1751", "1751", "Thr", "Thr", "T" ], [ "A2A654-1", "1751", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "NCARS-T-VTTTT", "1751", "1751", "Thr", "Thr", "T" ], [ "A2A654-1", "1751", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "22645316", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "NCARS-T-VTTTT", "1751", "1751", "Thr", "Thr", "T" ], [ "A2A654-1", "1753", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "ARSTV-T-TTTTT", "1753", "1753", "Thr", "Thr", "T" ], [ "A2A654-1", "1753", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "22645316", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "ARSTV-T-TTTTT", "1753", "1753", "Thr", "Thr", "T" ], [ "A2A654-1", "1754", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "RSTVT-T-TTTTV", "1754", "1754", "Thr", "Thr", "T" ], [ "A2A654-1", "1754", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "21606357", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "RSTVT-T-TTTTV", "1754", "1754", "Thr", "Thr", "T" ], [ "A2A654-1", "1755", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "STVTT-T-TTTVT", "1755", "1755", "Thr", "Thr", "T" ], [ "A2A654-1", "1755", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "21606357", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "STVTT-T-TTTVT", "1755", "1755", "Thr", "Thr", "T" ], [ "A2A654-1", "1755", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "STVTT-T-TTTVT", "1755", "1755", "Thr", "Thr", "T" ], [ "A2A654-1", "1755", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "22645316", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "STVTT-T-TTTVT", "1755", "1755", "Thr", "Thr", "T" ], [ "A2A654-1", "1756", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "TVTTT-T-TTVTK", "1756", "1756", "Thr", "Thr", "T" ], [ "A2A654-1", "1756", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "21606357", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "TVTTT-T-TTVTK", "1756", "1756", "Thr", "Thr", "T" ], [ "A2A654-1", "1757", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "VTTTT-T-TVTKL", "1757", "1757", "Thr", "Thr", "T" ], [ "A2A654-1", "1757", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "22645316", "protein_xref_oglcnac_db", "A2A654", "brain (synaptosome)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "MESH:D013574", "synaptosomes", "", "", "VTTTT-T-TVTKL", "1757", "1757", "Thr", "Thr", "T" ], [ "A2A654-1", "1760", "Thr", "G49108TO", "O-linked", "protein_xref_oglcnac_db", "A2A654", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "TTTTV-T-KLSTP", "1760", "1760", "Thr", "Thr", "T" ], [ "A2A654-1", "1760", "Thr", "G49108TO", "O-linked", "protein_xref_pubmed", "21606357", "protein_xref_oglcnac_db", "A2A654", "embryonic stem cells (ESCs)", "MS", "HTP", "", "GlcNAc", "O-GlcNAcylation", "", "", "", "", "TTTTV-T-KLSTP", "1760", "1760", "Thr", "Thr", "T" ] ] }, "readme": "Name\n - Mouse O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas)\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2023-02-24T16:22:06.506Z\n\nModified on\n - 2023-03-06T20:14:30.429Z\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]\n\nAuthors\n - Jungfeng Ma [junfeng.ma@georgetown.edu ]\n\nChecksum\n - \n\nUsability Domain\n - The Mouse O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas) contains mouse (taxid:10090) 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.\n\nDescription Domain\n Keywords\n - \n - O-GlcNAc\n - Serine\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 also maps the sample type to correct sample term id and sample term name. \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: mouse_protein_info_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_protein_info_uniprotkb.csv\n Name: mouse_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_protein_masterlist.csv\n Name: mouse_protein_recnames.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_protein_recnames.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/misc/sample_mapping.csv\n Name: ambiguous_sites_version_2.0.csv\n URI: /data/shared/glyds/downloads/atlas_oglcnac/2022_10_20/ambiguous_sites_version_2.0.csv\n Name: unambiguous_sites_version_2.0.csv\n URI: /data/shared/glyds/downloads/atlas_oglcnac/2022_10_20/unambiguous_sites_version_2.0.csv\n Name: cellosaurus.txt\n URI: /data/shared/glyds/downloads/cellosaurus/2023-03-21/cellosaurus.txt\n Output Subdomain\n Name: mouse_proteoform_glycosylation_sites_oglcnac_atlas.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_proteoform_glycosylation_sites_oglcnac_atlas.csv\n Name: mouse_proteoform_glycosylation_sites_oglcnac_atlas.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_proteoform_glycosylation_sites_oglcnac_atlas.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1363\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"1917\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"2\"\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: \"3\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"1423\"\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: \"1363\"\n Name: \"sample_type\"\n Description: \"\"\n Unique Values: \"37\"\n Name: \"method\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"analytical_throughput\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"notes\"\n Description: \"Notes\"\n Unique Values: \"124\"\n Name: \"carb_name\"\n Description: \"carbohydrate name\"\n Unique Values: \"1\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"12\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"12\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"14\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"14\"\n Name: \"peptide\"\n Description: \"Protein peptide\"\n Unique Values: \"4607\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"1917\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1917\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/mouse_proteoform_glycosylation_sites_oglcnac_atlas.csv" }