{ "bcoid": "GLY_000317", "title": "Mouse Protein PTM Annotation (UniProtKB)", "description": "The Mouse Protein PTM Annotation (UniProtKB) dataset contains mouse [taxid:10090] PTM annotations for ...", "filename": "mouse_protein_ptm_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Protein", "tags": "PTM annotation", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "B2RXV4-1...", "10429212..." ], [ "B2RXV4-1...", "MF_03203..." ] ], "headers": [ "uniprotkb_ca...", "pmid..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "pmid" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "ptm_annotation" } ], [ "B2RXV4-1", "10429212", "ECO_0000269", "N-Glycosylated." ], [ "B2RXV4-1", "MF_03203", "ECO_0000255", "N-Glycosylated." ], [ "B2RXV4-1", "MF_03206", "ECO_0000255", "N-Glycosylated." ], [ "B2RXV4-1", "P13500", "ECO_0000250", "N-Glycosylated." ], [ "B2RXV4-1", "P36897", "ECO_0000250", "N-Glycosylated." ], [ "B2RXV4-1", "15284223", "ECO_0000269", "N-Glycosylated." ], [ "B2RXV4-1", "18285349", "ECO_0000269", "N-Glycosylated." ], [ "B2RXV4-1", "Q14767", "ECO_0000250", "N-Glycosylated." ], [ "B2RXV4-1", "22237023", "ECO_0000269", "N-Glycosylated." ], [ "Q9QYH9-1", "P29965", "ECO_0000250", "The soluble form derives from the membrane form by proteolytic processing." ], [ "Q9QYH9-1", "O35789", "ECO_0000250", "The soluble form derives from the membrane form by proteolytic processing." ], [ "Q9QYH9-1", "P13721", "ECO_0000250", "The soluble form derives from the membrane form by proteolytic processing." ], [ "P52479-1", "", "", "Ubiquitinated. Deubiquitinated by USP13 (By similarity)." ], [ "P52479-1", "", "", "Phosphorylated by ATM following DNA damage, leading to stablization and translocation it to the nucleus." ], [ "O08537-1", "10230404", "ECO_0000269", "Phosphorylation at Ser-87 and Ser-105 recruits NCOA1." ], [ "O08537-1", "10995228", "ECO_0000269", "Phosphorylation at Ser-87 and Ser-105 recruits NCOA1." ], [ "Q3URK3-1", "23352454", "ECO_0000269", "Glycosylated. Interaction with OGT leads to GlcNAcylation." ], [ "Q9EP73-1", "Q9NZQ7", "ECO_0000250", "Ubiquitinated; STUB1 likely mediates polyubiquitination of PD-L1/CD274 triggering its degradation." ], [ "Q8R349-1", "", "", "Phosphorylated. Phosphorylation on Ser-560 occurs specifically during mitosis (By similarity)." ], [ "O08911-1", "20004242", "ECO_0000269", "Dually phosphorylated on Thr-183 and Tyr-185 by MAP2K3/MKK3 and MAP2K6/MKK6, which activates the enzyme." ], [ "O08911-1", "Q16539", "ECO_0000250", "Ubiquitinated. Ubiquitination leads to degradation by the proteasome pathway (By similarity)." ], [ "Q8BZM0-1", "Q53G59", "ECO_0000250", "Ubiquitinated by the SCF(FBXL17) complex, leading to its degradation by the proteaseome: ubiquitination by the SCF(FBXL17) complex takes place when aberrant BTB domain dimers are formed." ], [ "Q8BZM1-1", "12393607", "ECO_0000269", "Phosphorylated on tyrosine residues." ], [ "Q8BZM1-1", "19092807", "ECO_0000269", "Phosphorylated on tyrosine residues." ], [ "Q8BZM1-1", "11827461", "ECO_0000269", "Phosphorylated on tyrosine residues." ], [ "Q8BZM1-1", "11836526", "ECO_0000269", "Phosphorylated on tyrosine residues." ], [ "Q8BZM1-1", "Q14643", "ECO_0000250", "Phosphorylated on tyrosine residues." ], [ "Q8BZM1-1", "Q92990", "ECO_0000250", "Phosphorylated on tyrosine residues." ], [ "Q8BZM1-1", "P07722", "ECO_0000250", "Phosphorylated on tyrosine residues." ], [ "Q8BZM1-1", "9712903", "ECO_0000269", "Phosphorylated on tyrosine residues." ], [ "Q8BZM1-1", "9507023", "ECO_0000269", "Phosphorylated on tyrosine residues." ], [ "Q4VC33-1", "Q7L5Y9", "ECO_0000250", "Autoubiquitinated as component of the CTLH E3 ubiquitin-protein ligase complex (in vitro)." ], [ "P50429-1", "P08842", "ECO_0000250", "The conversion to 3-oxoalanine (also known as C-formylglycine, FGly), of a serine or cysteine residue in prokaryotes and of a cysteine residue in eukaryotes, is critical for catalytic activity." ], [ "P50429-1", "PIRSR036665-50", "ECO_0000256", "The conversion to 3-oxoalanine (also known as C-formylglycine, FGly), of a serine or cysteine residue in prokaryotes and of a cysteine residue in eukaryotes, is critical for catalytic activity." ], [ "Q99LV7-1", "19349973", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "16944957", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "Q12884", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "16007091", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "16002697", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "16537470", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "20006580", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "27922006", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "Q92954", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "16641094", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "Q9BY76", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "P09172", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "23027977", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "23041369", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "P10499", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "18712936", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "Q9NYG8", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "Q92633", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "P04629", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "O43692", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "25171405", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "7553896", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "7753172", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "20526344", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "P14151", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "10749671", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "17330941", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "16368742", "ECO_0000305", "N-glycosylated." ], [ "Q99LV7-1", "17803912", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "P20933", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "20043878", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "P41180", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "P41597", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "P19518", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "16314439", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "12874256", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "Q96D31", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "15665855", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "P84039", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "15676076", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "29909984", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "Q86Y38", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "22065762", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "21896731", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "P30989", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "Q16849", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "Q03431", "ECO_0000250", "N-glycosylated." ], [ "Q99LV7-1", "21911364", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "19557428", "ECO_0000269", "N-glycosylated." ], [ "Q99LV7-1", "20015956", "ECO_0000269", "N-glycosylated." ] ] }, "readme": "Name\n - Mouse Protein PTM Annotation (UniProtKB)\n\nVersion\n - 1.5.18\n\nCreated on\n - 2019-11-30T14:05:28.986536\n\nModified on\n - 2020-04-10T12:47:48.210199\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Mouse Protein PTM Annotation (UniProtKB) dataset contains mouse [taxid:10090] PTM annotations for UniProtKB canonical accessions. The annotation is the curated statements of mainly about glycosylation and phosphorylation. The dataset is derived form 2019-09 UniprotKB release. If you use this dataset please give proper attribution to UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - ptm annotation\n - glycosylation\n - phosphorylation\n\n Pipeline Steps\n - Step-1: The script extracts the ptm annotation strings from the triplestore for the UniProtKB canonical sequnces asnd extracts as a dataset in a csv format\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: uniprot-proteome-mus-musculus.nt\n URI: https://data.glygen.org/ln2wwwdata/reviewed/uniprot-proteome-mus-musculus.nt\n Name: mouse_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_masterlist.csv\n Output Subdomain\n Name: mouse_protein_ptm_annotation_uniprotkb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_ptm_annotation_uniprotkb.csv\n Name: mouse_protein_ptm_annotation_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_ptm_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"4256\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"7\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"3408\"\n Name: \"ptm_annotation\"\n Description: \"The Post Translational Modifiaction (PTM) annotation in UniProtKB that provides more context and description about the PTMs occuring on a proein\"\n Unique Values: \"4636\"", "downloadurl": "/ln2data/releases/data/v-1.5.18/reviewed/mouse_protein_ptm_annotation_uniprotkb.csv" }