{ "bcoid": "GLY_000321", "title": "Rat Protein Reactions (Reactome)", "description": "The Rat Protein Reactions (Reactome) dataset contains reactions information for pathways for rat [taxid:10116] ...", "filename": "rat_protein_reactions_reactome.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "Reactions Reactome", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "R-RNO-102212...", "ST3GAL4 tran..." ], [ "R-RNO-109639...", "Formation of..." ] ], "headers": [ "reaction_id...", "reaction_nam..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "reaction_id" }, { "type": "string", "label": "reaction_name" }, { "type": "string", "label": "cellular_location" }, { "type": "string", "label": "pmid" }, { "type": "string", "label": "pathway_id" } ], [ "R-RNO-1022129", "ST3GAL4 transfers Neu5Ac to terminal Gal of N-glycans", "Golgi membrane", "", "R-RNO-975577" ], [ "R-RNO-109639", "Formation of the closed pre-initiation complex", "Golgi membrane", "", "R-RNO-73779" ], [ "R-RNO-109700", "AKT2 binds PIP3", "Golgi membrane", "", "R-RNO-165158" ], [ "R-RNO-109702", "PDPK1 phosphorylates AKT2", "Golgi membrane", "", "R-RNO-165158" ], [ "R-RNO-110221", "Cleavage of uracil by SMUG1 glycosylase", "Golgi membrane", "", "R-RNO-110329" ], [ "R-RNO-110351", "Displacement of SMUG1 glycosylase by APEX1 at the AP site", "Golgi membrane", "", "R-RNO-110357" ], [ "R-RNO-111264", "Addition of nucleotides between position +11 and +30", "Golgi membrane", "", "R-RNO-73776" ], [ "R-RNO-111439", "Docking of Mature Histone mRNA complex:TAP at the NPC", "Golgi membrane", "", "R-RNO-159227" ], [ "R-RNO-111930", "Adenylate cyclase produces cAMP", "Golgi membrane", "", "R-RNO-163615" ], [ "R-RNO-112379", "Recruitment of elongation factors to form elongation complex", "Golgi membrane", "", "R-RNO-112382" ], [ "R-RNO-112383", "Hypophosphorylation of RNA Pol II CTD by FCP1P protein", "Golgi membrane", "", "R-RNO-113418" ], [ "R-RNO-112385", "Addition of nucleotides leads to transcript elongation", "Golgi membrane", "", "R-RNO-75955" ], [ "R-RNO-112392", "Resumption of elongation after recovery from pausing", "Golgi membrane", "", "R-RNO-674695" ], [ "R-RNO-112395", "Abortive termination of elongation after arrest", "Golgi membrane", "", "R-RNO-674695" ], [ "R-RNO-112396", "Separation of elongating transcript from template", "Golgi membrane", "", "R-RNO-75955" ], [ "R-RNO-112430", "Formation of P-TEFb complex", "Golgi membrane", "", "R-RNO-674695" ], [ "R-RNO-113411", "2-4 nt.backtracking of Pol II complex on the template leading to elongation pausing", "Golgi membrane", "", "R-RNO-674695" ], [ "R-RNO-113412", "Pol II elongation complex moves on the template as transcript elongates", "Golgi membrane", "", "R-RNO-75955" ], [ "R-RNO-113413", "TFIIS-mediated recovery of elongation from arrest", "Golgi membrane", "", "R-RNO-674695" ], [ "R-RNO-113414", "7-14 nt. Backtracking of Pol II complex on the template leading to elongation arrest", "Golgi membrane", "", "R-RNO-674695" ], [ "R-RNO-113430", "Extrusion of 5'-end of 30 nt long transcript through the pore in Pol II complex", "Golgi membrane", "", "R-RNO-77075" ], [ "R-RNO-114352", "Sequestration of tBID by BCL-2", "Golgi membrane", "", "R-RNO-111453" ], [ "R-RNO-114684", "Phosphorylation of Syntaxin-4", "Golgi membrane", "", "R-RNO-114516" ], [ "R-RNO-1168633", "NF-kappaB translocates from the cytosol to the nucleus", "Golgi membrane", "", "R-RNO-1169091" ], [ "R-RNO-1168638", "Activated IKK phosphorylates I-kappaB", "Golgi membrane", "", "R-RNO-1169091" ], [ "R-RNO-1168640", "Ubiquitinated IkB is degraded", "Golgi membrane", "", "R-RNO-1169091" ], [ "R-RNO-1168642", "SCF with beta-TrCP1 or beta-TrCP2 binds NF-kappaB:phospho-IkB", "Golgi membrane", "", "R-RNO-1169091" ], [ "R-RNO-1168643", "SCF-beta-TrCP ubiquitinylates IkB", "Golgi membrane", "", "R-RNO-1169091" ], [ "R-RNO-1225919", "Phospho R-SMAD(SMAD2/3):CO-SMAD(SMAD4):FOXH1 binds Activin Response Element", "Golgi membrane", "", "R-RNO-1181150" ], [ "R-RNO-1234159", "Proteasome proteolyzes ub-HIF-alpha", "Golgi membrane", "", "R-RNO-1234176" ], [ "R-RNO-1236970", "Proteasomal clevage of exogenous antigen", "Golgi membrane", "", "R-RNO-1236978" ], [ "R-RNO-1254248", "Translocation of ERBB4s80:YAP1 complex to the nucleus", "Golgi membrane", "", "R-RNO-1251985" ], [ "R-RNO-1254251", "ERBB4s80 binds YAP1", "Golgi membrane", "", "R-RNO-1251985" ], [ "R-RNO-1358791", "Phosphorylation of USP8 by P-AKT", "Golgi membrane", "", "R-RNO-1358803" ], [ "R-RNO-139893", "Granzyme-B activates BID by cleavage", "Golgi membrane", "", "R-RNO-75108" ], [ "R-RNO-139895", "tBID activates BAK protein", "Golgi membrane", "", "R-RNO-111452" ], [ "R-RNO-139897", "BAD displaces tBID from BCL-2 sequestration", "Golgi membrane", "", "R-RNO-111447" ], [ "R-RNO-139898", "Caspase-8 activates BID by cleavage", "Golgi membrane", "", "R-RNO-75108" ], [ "R-RNO-139908", "Phosphorylation of DLC2 by MAPK8", "Golgi membrane", "", "R-RNO-139910" ], [ "R-RNO-139909", "Translocation of BMF to mitochondria", "Golgi membrane", "", "R-RNO-139910" ], [ "R-RNO-139917", "tBID activates BAX protein", "Golgi membrane", "", "R-RNO-114294" ], [ "R-RNO-139920", "Translocation of tBID to mitochondria", "Golgi membrane", "", "R-RNO-75108" ], [ "R-RNO-140978", "TRADD:TRAF2:RIP1 complex binds FADD", "Golgi membrane", "", "R-RNO-5357786" ], [ "R-RNO-141156", "TRAIL-mediated dimerization of procaspase-8", "Golgi membrane", "", "R-RNO-69416" ], [ "R-RNO-141159", "TNF-mediated dimerization of procaspase-8", "Golgi membrane", "", "R-RNO-69416" ], [ "R-RNO-141200", "MAOB:FAD oxidatively deaminates of PEA", "Golgi membrane", "", "R-RNO-141333" ], [ "R-RNO-141202", "MAOB:FAD oxidatively deaminates TYR", "Golgi membrane", "", "R-RNO-141333" ], [ "R-RNO-141367", "Myristoylation of tBID by NMT1", "Golgi membrane", "", "R-RNO-75108" ], [ "R-RNO-1433506", "Phosphorylation of APS", "Golgi membrane", "", "R-RNO-1433559" ], [ "R-RNO-1475022", "Carbonic anhydrase dehydrates bicarbonate (cytosol)", "Golgi membrane", "", "R-RNO-1475029" ], [ "R-RNO-1475026", "Carbonic anhydrase hydrates carbon dioxide (cytosol)", "Golgi membrane", "", "R-RNO-1475029" ], [ "R-RNO-1475435", "Carbonic anhydrase I/II hydrates carbon dioxide", "Golgi membrane", "", "R-RNO-1237044" ], [ "R-RNO-1475436", "Carbonic anhydrase I/II dehydrates bicarbonate", "Golgi membrane", "", "R-RNO-1247673" ], [ "R-RNO-1482973", "CDP-Cho and DAG are converted to PC by CHPT1 at the Golgi membrane", "Golgi membrane", "", "R-RNO-1483191" ], [ "R-RNO-1497784", "The cofactor BH4 is required for electron transfer in the eNOS catalytic cycle", "Golgi membrane", "", "R-RNO-5218920" ], [ "R-RNO-1497796", "BH2 binding can lead to eNOS uncoupling", "Golgi membrane", "", "R-RNO-1474151" ], [ "R-RNO-1497810", "Uncoupled eNOS favours the formation of superoxide", "Golgi membrane", "", "R-RNO-203615" ], [ "R-RNO-1504193", "Ubiquitinated DVL is degraded by the proteasome", "Golgi membrane", "", "R-RNO-4641258" ], [ "R-RNO-1535903", "Phospho R-SMAD(SMAD2/3):CO-SMAD(SMAD4):FOXO3 binds FoxO3a-binding elements", "Golgi membrane", "", "R-RNO-1181150" ], [ "R-RNO-1549526", "Phosphorylation of SMAD2/3 by Activin:Activin Receptor", "Golgi membrane", "", "R-RNO-1502540" ], [ "R-RNO-156808", "Formation of translation initiation complexes yielding circularized Ceruloplasmin mRNA in a 'closed-loop' conformation", "Golgi membrane", "", "R-RNO-72649" ], [ "R-RNO-156823", "Association of phospho-L13a with GAIT element of Ceruloplasmin mRNA", "Golgi membrane", "", "R-RNO-156827" ], [ "R-RNO-156826", "Dissociation of L13a from the 60s ribosomal subunit", "Golgi membrane", "", "R-RNO-156827" ], [ "R-RNO-157849", "Formation of translation initiation complexes containing mRNA that does not circularize", "Golgi membrane", "", "R-RNO-72649" ], [ "R-RNO-158441", "Transport of the Mature intronless transcript derived mRNA:TAP:Aly/Ref Complex through the NPC", "Golgi membrane", "", "R-RNO-159231" ], [ "R-RNO-158447", "Release of the Mature intronless derived mRNA, TAP, and Aly/Ref from the NPC", "Golgi membrane", "", "R-RNO-159231" ], [ "R-RNO-158481", "Transport of the Mature Intronless Transcript Derived Histone mRNA:TAP:Aly/Ref Complex through the NPC", "Golgi membrane", "", "R-RNO-159227" ], [ "R-RNO-158484", "Release of the SLBP independent Histone mRNA from the NPC", "Golgi membrane", "", "R-RNO-159227" ], [ "R-RNO-159046", "Transport of the Mature IntronlessTranscript Derived Histone mRNA:SLBP:TAP:Aly/Ref complex through the NPC", "Golgi membrane", "", "R-RNO-159230" ], [ "R-RNO-159050", "Release of the Mature intronless transcript derived Histone mRNA:SLBP:eIF4E Complex", "Golgi membrane", "", "R-RNO-159230" ], [ "R-RNO-159101", "NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)", "Golgi membrane", "", "R-RNO-159236" ], [ "R-RNO-159431", "Cytosolic chenodeoxycholoyl-CoA or choloyl-CoA are conjugated with glycine or taurine", "Golgi membrane", "", "R-RNO-159418" ], [ "R-RNO-159752", "GGCX gamma-carboxylates PROS1(25-676) (pro-protein S)", "Golgi membrane", "", "R-RNO-159740" ], [ "R-RNO-159761", "GGCX gamma-carboxylates F7(21-466) (pro-factor VII)", "Golgi membrane", "", "R-RNO-159740" ], [ "R-RNO-159795", "GGCX gamma-carboxylates 3D-PROC(33-197) (pro-protein C light chain)", "Golgi membrane", "", "R-RNO-159740" ], [ "R-RNO-159803", "GGCX gamma-carboxylates 3D-F9(29-461) (pro-factor IX)", "Golgi membrane", "", "R-RNO-159740" ], [ "R-RNO-159819", "GGCX gamma-carboxylates 3D-F10(32-179) (pro-factor X light chain)", "Golgi membrane", "", "R-RNO-159740" ], [ "R-RNO-159826", "GGCX gamma-carboxylates F2(25-622) (pro-prothrombin)", "Golgi membrane", "", "R-RNO-159740" ], [ "R-RNO-1614567", "Excess homocysteine yields homolanthionine and H2S", "Golgi membrane", "", "R-RNO-1614558" ], [ "R-RNO-1614583", "PXLP-K212-CTH cleaves L-Cystathionine", "Golgi membrane", "", "R-RNO-1614603" ], [ "R-RNO-1614591", "Excess cysteine yields lanthionine and H2S", "Golgi membrane", "", "R-RNO-1614558" ], [ "R-RNO-1614614", "Cysteine is degraded to serine and H2S", "Golgi membrane", "", "R-RNO-1614558" ], [ "R-RNO-1614631", "Homocysteine is degraded to oxobutanoate and H2S", "Golgi membrane", "", "R-RNO-1614558" ], [ "R-RNO-1614654", "BHMT tetramer transfers CH3 group from BET to HCYS to form DMGLY", "Golgi membrane", "", "R-RNO-1614635" ] ] }, "readme": "Name\n - Rat Protein Reactions (Reactome)\n\nVersion\n - 1.7.10\n\nCreated on\n - 2019-11-30T15:08:38.029791\n\nModified on\n - 2020-04-10T12:14:22.002556\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 Rat Protein Reactions (Reactome) dataset contains reactions information for pathways for rat [taxid:10116] UniProtKB accessions that includes reaction participants, pathway ID, reaction ID, PMID etc from Reactome database. 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\nDescription Domain\n Keywords\n - Reactome\n - Pathway\n - Reactions\n - PMID\n\n Pipeline Steps\n - Step-1: The script loads the Reactome reaction data from the triplestore containing triples from nt file to retrieve the information associated with the Reactome IDs and maps it to the UniProtKB canonical accessions and extracts the dataset in the 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/ln2data/releases/data/v-1.7.10/source/uniprot-proteome-mus-musculus.nt\n Name: rat_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.7.10/reviewed/rat_protein_masterlist.csv\n Output Subdomain\n Name: rat_protein_reactions_reactome.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.7.10/reviewed/rat_protein_reactions_reactome.csv\n Name: rat_protein_reactions_reactome.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.7.10/reviewed/rat_protein_reactions_reactome.stat.csv\n\nFields\n Name: \"reaction_id\"\n Description: \"The identifier assigned to a reaction in Reactome database\"\n Unique Values: \"7477\"\n Name: \"reaction_name\"\n Description: \"The name assigned to a reaction in Reactome database\"\n Unique Values: \"7455\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"2\"\n Name: \"pathway_id\"\n Description: \"Pathway Identifier\"\n Unique Values: \"1253\"\n Name: \"cellular_location\"\n Description: \"The loaction in the cell where reaction occurs\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.7.10/reviewed/rat_protein_reactions_reactome.csv" }