{ "bcoid": "GLY_000877", "title": "Dicty UniProtKB Xref Reactome", "description": "The Dicty UniProtKB Xref Reactome contains dicty [taxid:44689] UniProtKB canonical accessions cross-referenced ...", "filename": "dicty_protein_xref_reactome.csv", "filetype": "csv", "categories": { "species": [ "Dictyostelium discoideum" ], "molecule": [ "Protein" ], "tag": [ "Reactome cross-references" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q54PT2-1...", "protein_xref..." ], [ "Q54PT2-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "xref_label" } ], [ "Q54PT2-1", "protein_xref_reactome", "R-DDI-917729", "Endosomal Sorting Complex Required For Transport (ESCRT)" ], [ "Q54PT2-1", "protein_xref_reactome", "R-DDI-9668328", "Sealing of the nuclear envelope (NE) by ESCRT-III" ], [ "Q54PT7-1", "protein_xref_reactome", "R-DDI-5683826", "Surfactant metabolism" ], [ "Q54PT7-1", "protein_xref_reactome", "R-DDI-5683826", "Surfactant metabolism" ], [ "Q54PT7-1", "protein_xref_reactome", "R-DDI-5683826", "Surfactant metabolism" ], [ "Q54N47-1", "protein_xref_reactome", "R-DDI-70895", "Branched-chain amino acid catabolism" ], [ "Q54N47-1", "protein_xref_reactome", "R-DDI-70895", "Branched-chain amino acid catabolism" ], [ "Q54N47-1", "protein_xref_reactome", "R-DDI-70895", "Branched-chain amino acid catabolism" ], [ "Q54N47-1", "protein_xref_reactome", "R-DDI-70895", "Branched-chain amino acid catabolism" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-8866654", "E3 ubiquitin ligases ubiquitinate target proteins" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-8866654", "E3 ubiquitin ligases ubiquitinate target proteins" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-9033241", "Peroxisomal protein import" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-9033241", "Peroxisomal protein import" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-9033241", "Peroxisomal protein import" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-9033241", "Peroxisomal protein import" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-9033241", "Peroxisomal protein import" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-9033241", "Peroxisomal protein import" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-9033241", "Peroxisomal protein import" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-9603798", "Class I peroxisomal membrane protein import" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-9603798", "Class I peroxisomal membrane protein import" ], [ "Q54N40-1", "protein_xref_reactome", "R-DDI-9603798", "Class I peroxisomal membrane protein import" ], [ "Q54N41-1", "protein_xref_reactome", "R-DDI-6781823", "Formation of TC-NER Pre-Incision Complex" ], [ "Q54N41-1", "protein_xref_reactome", "R-DDI-6782135", "Dual incision in TC-NER" ], [ "Q54N41-1", "protein_xref_reactome", "R-DDI-6782135", "Dual incision in TC-NER" ], [ "Q54N41-1", "protein_xref_reactome", "R-DDI-6782135", "Dual incision in TC-NER" ], [ "Q54N41-1", "protein_xref_reactome", "R-DDI-6782135", "Dual incision in TC-NER" ], [ "Q54N41-1", "protein_xref_reactome", "R-DDI-6782210", "Gap-filling DNA repair synthesis and ligation in TC-NER" ], [ "Q54N41-1", "protein_xref_reactome", "R-DDI-6782135", "Dual incision in TC-NER" ], [ "Q54N41-1", "protein_xref_reactome", "R-DDI-72163", "mRNA Splicing - Major Pathway" ], [ "Q54N41-1", "protein_xref_reactome", "R-DDI-6782210", "Gap-filling DNA repair synthesis and ligation in TC-NER" ], [ "Q54N49-1", "protein_xref_reactome", "R-DDI-1855183", "Synthesis of IP2, IP, and Ins in the cytosol" ], [ "Q54QV4-1", "protein_xref_reactome", "R-DDI-6791226", "Major pathway of rRNA processing in the nucleolus and cytosol" ], [ "Q54QV4-1", "protein_xref_reactome", "R-DDI-6791226", "Major pathway of rRNA processing in the nucleolus and cytosol" ], [ "Q55BJ9-1", "protein_xref_reactome", "R-DDI-3299685", "Detoxification of Reactive Oxygen Species" ], [ "Q55BJ9-1", "protein_xref_reactome", "R-DDI-2151201", "Transcriptional activation of mitochondrial biogenesis" ], [ "Q55BJ2-1", "protein_xref_reactome", "R-DDI-429958", "mRNA decay by 3' to 5' exoribonuclease" ], [ "Q55BJ2-1", "protein_xref_reactome", "R-DDI-450385", "Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA" ], [ "Q55BJ2-1", "protein_xref_reactome", "R-DDI-450513", "Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA" ], [ "Q55BJ2-1", "protein_xref_reactome", "R-DDI-6791226", "Major pathway of rRNA processing in the nucleolus and cytosol" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-1660514", "Synthesis of PIPs at the Golgi membrane" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-1660514", "Synthesis of PIPs at the Golgi membrane" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-199992", "trans-Golgi Network Vesicle Budding" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-5620916", "VxPx cargo-targeting to cilium" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6807878", "COPI-mediated anterograde transport" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6807878", "COPI-mediated anterograde transport" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6807878", "COPI-mediated anterograde transport" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6807878", "COPI-mediated anterograde transport" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6807878", "COPI-mediated anterograde transport" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6811434", "COPI-dependent Golgi-to-ER retrograde traffic" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6811434", "COPI-dependent Golgi-to-ER retrograde traffic" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6811434", "COPI-dependent Golgi-to-ER retrograde traffic" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6811434", "COPI-dependent Golgi-to-ER retrograde traffic" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6811434", "COPI-dependent Golgi-to-ER retrograde traffic" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6811438", "Intra-Golgi traffic" ], [ "Q54JJ3-1", "protein_xref_reactome", "R-DDI-6811438", "Intra-Golgi traffic" ], [ "Q54GS8-1", "protein_xref_reactome", "R-DDI-76061", "RNA Polymerase III Transcription Initiation From Type 1 Promoter" ], [ "Q54GS8-1", "protein_xref_reactome", "R-DDI-76061", "RNA Polymerase III Transcription Initiation From Type 1 Promoter" ], [ "Q54GS8-1", "protein_xref_reactome", "R-DDI-76061", "RNA Polymerase III Transcription Initiation From Type 1 Promoter" ], [ "Q54GS8-1", "protein_xref_reactome", "R-DDI-76066", "RNA Polymerase III Transcription Initiation From Type 2 Promoter" ], [ "Q54GS8-1", "protein_xref_reactome", "R-DDI-76066", "RNA Polymerase III Transcription Initiation From Type 2 Promoter" ], [ "Q54GS8-1", "protein_xref_reactome", "R-DDI-76066", "RNA Polymerase III Transcription Initiation From Type 2 Promoter" ], [ "Q86K94-1", "protein_xref_reactome", "R-DDI-204005", "COPII-mediated vesicle transport" ], [ "Q86K94-1", "protein_xref_reactome", "R-DDI-204005", "COPII-mediated vesicle transport" ], [ "Q86K94-1", "protein_xref_reactome", "R-DDI-8876198", "RAB GEFs exchange GTP for GDP on RABs" ], [ "Q86K94-1", "protein_xref_reactome", "R-DDI-204005", "COPII-mediated vesicle transport" ], [ "Q86K93-1", "protein_xref_reactome", "R-DDI-1632852", "Macroautophagy" ], [ "Q86K93-1", "protein_xref_reactome", "R-DDI-917729", "Endosomal Sorting Complex Required For Transport (ESCRT)" ], [ "Q86K93-1", "protein_xref_reactome", "R-DDI-917729", "Endosomal Sorting Complex Required For Transport (ESCRT)" ], [ "Q86K93-1", "protein_xref_reactome", "R-DDI-9668328", "Sealing of the nuclear envelope (NE) by ESCRT-III" ], [ "Q86K93-1", "protein_xref_reactome", "R-DDI-9668328", "Sealing of the nuclear envelope (NE) by ESCRT-III" ], [ "Q86K93-1", "protein_xref_reactome", "R-DDI-9668328", "Sealing of the nuclear envelope (NE) by ESCRT-III" ], [ "Q86K93-1", "protein_xref_reactome", "R-DDI-9668328", "Sealing of the nuclear envelope (NE) by ESCRT-III" ], [ "Q86K93-1", "protein_xref_reactome", "R-DDI-9668328", "Sealing of the nuclear envelope (NE) by ESCRT-III" ], [ "Q86K90-1", "protein_xref_reactome", "R-DDI-429958", "mRNA decay by 3' to 5' exoribonuclease" ], [ "Q9U3X4-1", "protein_xref_reactome", "R-DDI-71403", "Citric acid cycle (TCA cycle)" ], [ "Q54WP9-1", "protein_xref_reactome", "R-DDI-72163", "mRNA Splicing - Major Pathway" ], [ "Q54KL5-1", "protein_xref_reactome", "R-DDI-8951664", "Neddylation" ], [ "Q54KL5-1", "protein_xref_reactome", "R-DDI-8951664", "Neddylation" ], [ "Q54KL5-1", "protein_xref_reactome", "R-DDI-8951664", "Neddylation" ], [ "Q54KL5-1", "protein_xref_reactome", "R-DDI-8951664", "Neddylation" ], [ "Q54KL5-1", "protein_xref_reactome", "R-DDI-8951664", "Neddylation" ], [ "Q54KL5-1", "protein_xref_reactome", "R-DDI-9772755", "Formation of WDR5-containing histone-modifying complexes" ], [ "Q54KL5-1", "protein_xref_reactome", "R-DDI-9772755", "Formation of WDR5-containing histone-modifying complexes" ], [ "Q54KL5-1", "protein_xref_reactome", "R-DDI-3214858", "RMTs methylate histone arginines" ] ] }, "readme": "Name\n - Dicty UniProtKB Xref Reactome\n\nVersion\n - v-2.4.1\n\nCreated on\n - \n\nModified on\n - 2024-01-09T05:48:13\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Dicty UniProtKB Xref Reactome contains dicty [taxid:44689] UniProtKB canonical accessions cross-referenced to Reactome database accessions/identifiers. The dataset is derived from 2019-09 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\",\n REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database.\n\nDescription Domain\n Keywords\n - pathways\n - reactions\n - REACTOME\n - cross-reference\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are cross-referenced to REACTOME database accessions/identifiers from the triplestore containing triples from nt file and extracts the data as a csv dataset.\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: uniprot-proteome-dictyostelium-discoideum.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2024_02_13/uniprot-proteome-dictyostelium-discoideum.nt\n Output Subdomain\n Name: dicty_protein_xref_reactome.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/dicty_protein_xref_reactome.csv\n Name: dicty_protein_xref_reactome.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/dicty_protein_xref_reactome.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"2612\"\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: \"697\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"697\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/dicty_protein_xref_reactome.csv" }