{ "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-75238...", "TRAIL binds ..." ], [ "R-RNO-158118...", "factor VIII ..." ] ], "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-75238", "TRAIL binds TRAIL receptors", "plasma membrane", "", "R-RNO-75158" ], [ "R-RNO-158118", "factor VIII + von Willebrand factor multimer -> factor VIII:von Willibrand factor multimer", "plasma membrane", "", "R-RNO-140837" ], [ "R-RNO-73812", "FGAR + L-Glutamine + ATP + H2O => FGAM + L-Glutamate + ADP + Pi", "plasma membrane", "", "R-RNO-73817" ], [ "R-RNO-9661625", "FVIII is secreted", "plasma membrane", "", "R-RNO-140837" ], [ "R-RNO-9670014", "Factor VIIIa dissociates ", "plasma membrane", "", "R-RNO-140837" ], [ "R-RNO-9614271", "Autocleavage of ADGRG6", "plasma membrane", "", "R-RNO-9619665" ], [ "R-RNO-9614273", "ADGRG heterodimer translocates to plasma membrane", "plasma membrane", "", "R-RNO-9619665" ], [ "R-RNO-9673053", "PM20D1 transforms oleoyl-phe from oleate and phe", "plasma membrane", "", "R-RNO-9673163" ], [ "R-RNO-9673054", "PM20D1 hydrolyzes oleoyl-phe", "plasma membrane", "", "R-RNO-9673163" ], [ "R-RNO-9674531", "AAMP binds EGFR", "plasma membrane", "", "R-RNO-177929" ], [ "R-RNO-109955", "Formation of ERCC1:XPF heterodimeric complex", "plasma membrane", "", "R-RNO-5696395" ], [ "R-RNO-9668335", "CHMP7 binds LEMD2", "plasma membrane", "", "R-RNO-9668328" ], [ "R-RNO-9676160", "AAMP binds NOD2", "plasma membrane", "", "R-RNO-168638" ], [ "R-RNO-216072", "Interaction of integrin alphaIIbbeta3 with von Willebrand factor", "plasma membrane", "", "R-RNO-216083" ], [ "R-RNO-265425", "Interaction of integrin alphaVbeta3 with von Willbrand Factor", "plasma membrane", "", "R-RNO-216083" ], [ "R-RNO-8944232", "Association of procollagen type XII", "plasma membrane", "", "R-RNO-8948216" ], [ "R-RNO-163670", "Nuclear transport of pChREBP (Thr 666) protein", "plasma membrane", "", "R-RNO-163358" ], [ "R-RNO-164423", "PhosphoChREBP (Thr 666) is exported to cytosol", "plasma membrane", "", "R-RNO-163358" ], [ "R-RNO-2168046", "Collagen type XII degradation by MMP12", "plasma membrane", "", "R-RNO-1442490" ], [ "R-RNO-350869", "Thyroxine is deiodinated to reverse triiodothyronine (RT3)", "plasma membrane", "", "R-RNO-350864" ], [ "R-RNO-5675206", "PEA15 binds MAPK monomers and dimers", "plasma membrane", "", "R-RNO-112409" ], [ "R-RNO-5685606", "CLEC2D binds KLRB1", "plasma membrane", "", "R-RNO-198933" ], [ "R-RNO-9627089", "CASP9 is phosphorylated at T125", "plasma membrane", "", "R-RNO-9627069" ], [ "R-RNO-9635739", "PTPN7 dephosphorylates p-T,Y-MAPKs", "plasma membrane", "", "R-RNO-5675221" ], [ "R-RNO-9635743", "PTPN7 binds p-T,Y-MAPK", "plasma membrane", "", "R-RNO-5675221" ], [ "R-RNO-9653503", "KRAS4B is phosphorylated on serine 181", "plasma membrane", "", "R-RNO-9648002" ], [ "R-RNO-9668395", "CHMP7 binds CC2D1B", "plasma membrane", "", "R-RNO-9668328" ], [ "R-RNO-9674093", "PDGFRs bind type I TKI", "plasma membrane", "", "R-RNO-186797" ], [ "R-RNO-9674095", "PDGFRs bind type II TKI", "plasma membrane", "", "R-RNO-186797" ], [ "R-RNO-5674018", "BRAP binds RAS:GTP", "plasma membrane", "", "R-RNO-5675221" ], [ "R-RNO-8865182", "OTUD7A hydrolyses K11diUb", "plasma membrane", "", "R-RNO-5689896" ], [ "R-RNO-8938951", "RUNX1 binds PAX5 (BSAP)", "plasma membrane", "", "R-RNO-8939245" ], [ "R-RNO-9607304", "SOS1-mediated nucleotide exchange of RAS donwstream of FLT3", "plasma membrane", "", "R-RNO-5673001" ], [ "R-RNO-9612219", "ERBB4s80 binds to SRC", "plasma membrane", "", "R-RNO-1253288" ], [ "R-RNO-9641096", "Misfolded proteins bind PRKN:UBE2N:UBE2V1:Ub", "plasma membrane", "", "R-RNO-9646399" ], [ "R-RNO-9641111", "Parkin transfers Ub to misfolded proteins", "plasma membrane", "", "R-RNO-9646399" ], [ "R-RNO-9641127", "Ub:misfolded proteins polymerize to PolyUb:misfolded proteins", "plasma membrane", "", "R-RNO-9646399" ], [ "R-RNO-9646348", "PolyUb-Misfolded Proteins:HDAC6 bind dynein motor", "plasma membrane", "", "R-RNO-9646399" ], [ "R-RNO-9656891", "OPN1SW binds 11cRAL", "plasma membrane", "", "R-RNO-2187335" ], [ "R-RNO-9661397", "SLCO1B1 transports BIL from extracellular region (blood) to cytosol (hepatocyte)", "plasma membrane", "", "R-RNO-189483" ], [ "R-RNO-9661799", "SLCO1B3 transports BIL from extracellular region (blood) to cytosol (hepatocyte)", "plasma membrane", "", "R-RNO-189483" ], [ "R-RNO-9663492", "BIL dissociates from GSTA1, FABP1", "plasma membrane", "", "R-RNO-189483" ], [ "R-RNO-9663511", "BIL binds GSTA1, FABP1", "plasma membrane", "", "R-RNO-189483" ], [ "R-RNO-1449687", "Corticosteroids bind to CBG in blood", "plasma membrane", "", "R-RNO-194002" ], [ "R-RNO-177157", "phenylacetate + Coenzyme A + ATP => phenylacetyl-CoA + AMP + pyrophosphate", "plasma membrane", "", "R-RNO-177162" ], [ "R-RNO-210282", "Interaction of GPVI and FceRI gamma", "plasma membrane", "", "R-RNO-75892" ], [ "R-RNO-2168079", "MASTL (GWL) phosphorylates ARPP19", "plasma membrane", "", "R-RNO-2465910" ], [ "R-RNO-75883", "DHRS7B reduces GO3P to HXDG3P", "plasma membrane", "", "R-RNO-75896" ], [ "R-RNO-9648983", "HTR3A pentamer:5HT transports Na+,K+,Ca2+", "plasma membrane", "", "R-RNO-112314" ], [ "R-RNO-9649108", "HTR3A pentamer binds 5HT", "plasma membrane", "", "R-RNO-112314" ], [ "R-RNO-9661417", "ABCG2 tetramer transports BMG,BDG from cytosol to extracellular region", "plasma membrane", "", "R-RNO-189483" ], [ "R-RNO-109278", "NT5E:Zn2+ hydrolyses AMP,dAMP,GMP, IMP", "plasma membrane", "", "R-RNO-74259" ], [ "R-RNO-109387", "(d)AMP, (d)GMP, or (d)IMP + H2O => (deoxy)adenosine, (deoxy)guanosine, or (deoxy)inosine + orthophosphate (NT5C1A)", "plasma membrane", "", "R-RNO-74259" ], [ "R-RNO-109415", "AMP + H2O => adenosine + orthophosphate [NT5C1B]", "plasma membrane", "", "R-RNO-74259" ], [ "R-RNO-109470", "(d)GMP or (d)IMP + H2O => (d)G or (d)I + orthophosphate (NT5C)", "plasma membrane", "", "R-RNO-74259" ], [ "R-RNO-109624", "(2'-deoxy)adenosine + ATP => (d)AMP + ADP (ADK)", "plasma membrane", "", "R-RNO-74217" ], [ "R-RNO-109671", "deoxyadenosine or deoxyguanosine + ATP => dAMP or dGMP + ADP (DCK)", "plasma membrane", "", "R-RNO-74217" ], [ "R-RNO-109699", "PI3K-containing complexes phosphorylate PIP2 to PIP3", "plasma membrane", "", "R-RNO-109704" ], [ "R-RNO-109759", "deoxycytidine, thymidine, or deoxyuridine + ATP => dCMP, TMP, or dUMP + ADP [TK2]", "plasma membrane", "", "R-RNO-73614" ], [ "R-RNO-109822", "MAPK3,(MAPK1) phosphorylates GRB2-1:SOS1:p-Y427-SHC1", "plasma membrane", "", "R-RNO-74749" ], [ "R-RNO-109823", "MAPK3,(MAPK1) phosphorylates GRB2-1:SOS1:p-Y-IRS1,p-Y-IRS2", "plasma membrane", "", "R-RNO-74749" ], [ "R-RNO-109857", "MAP2K1 binds MAPK3", "plasma membrane", "", "R-RNO-110056" ], [ "R-RNO-109858", "MAP2K2 binds MAPK1", "plasma membrane", "", "R-RNO-112411" ], [ "R-RNO-109863", "Dissociation of p-T,Y-MAPK3:MAP2K1", "plasma membrane", "", "R-RNO-110056" ], [ "R-RNO-109864", "Dissociation of p-T,Y-MAPK1:p-S,T-MAP2K2", "plasma membrane", "", "R-RNO-112411" ], [ "R-RNO-109903", "cytidine or uridine + ATP => CMP or UMP + ADP [UCK2]", "plasma membrane", "", "R-RNO-73614" ], [ "R-RNO-110011", "Binding of Grb10 to the insulin receptor", "plasma membrane", "", "R-RNO-74749" ], [ "R-RNO-110359", "APEX1 mediates endonucleolytic cleavage at the 5' side of the AP site", "plasma membrane", "", "R-RNO-73933" ], [ "R-RNO-110360", "Recruitment of POLB to the AP site", "plasma membrane", "", "R-RNO-73930" ], [ "R-RNO-110375", "Excision of the abasic sugar phosphate (5'dRP) residue at the single strand break", "plasma membrane", "", "R-RNO-73930" ], [ "R-RNO-110376", "Recruitment of LIG3:XRCC1 complex to the site of repair by POLB", "plasma membrane", "", "R-RNO-110381" ], [ "R-RNO-111253", "POLB incorporates the first 3' dNMP and displaces 5'ddRP at SSB site", "plasma membrane", "", "R-RNO-5651801" ], [ "R-RNO-111285", "Formation of phosphoribosyl pyrophosphate amidotransferase tetramer", "plasma membrane", "", "R-RNO-73817" ], [ "R-RNO-111289", "Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer", "plasma membrane", "", "R-RNO-73817" ], [ "R-RNO-111438", "Recruitment of U7 snRNP:ZFP100 complex to the Histone Pre-mRNA", "plasma membrane", "", "R-RNO-111367" ], [ "R-RNO-111524", "IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]", "plasma membrane", "", "R-RNO-73817" ], [ "R-RNO-112033", "hypoxanthine + (deoxy)ribose 1-phosphate <=> (deoxy)inosine + orthophosphate (NP)", "plasma membrane", "", "R-RNO-74217" ], [ "R-RNO-112034", "guanine + (deoxy)ribose 1-phosphate <=> (deoxy)guanosine + orthophosphate (NP)", "plasma membrane", "", "R-RNO-74217" ], [ "R-RNO-112266", "thymine or uracil + 2-deoxy-D-ribose 1-phosphate <=> thymidine or deoxyuridine + orthophosphate [TYMP]", "plasma membrane", "", "R-RNO-73614" ], [ "R-RNO-112342", "Inactivation of MAP2K1 by CDK1", "plasma membrane", "", "R-RNO-110056" ], [ "R-RNO-114553", "Activation of conventional Protein Kinase C", "plasma membrane", "", "R-RNO-76005" ], [ "R-RNO-1168445", "PTP1B binds the GH receptor complex", "plasma membrane", "", "R-RNO-982772" ], [ "R-RNO-1168459", "Lyn activates ERK", "plasma membrane", "", "R-RNO-982772" ], [ "R-RNO-1168894", "p-STAT5A/B dissociates from the Growth Hormone receptor", "plasma membrane", "", "R-RNO-982772" ] ] }, "readme": "Name\n - Rat Protein Reactions (Reactome)\n\nVersion\n - 1.8.24\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-1.8.24/source/uniprot-proteome-mus-musculus.nt\n Name: rat_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.24/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-1.8.24/reviewed/rat_protein_reactions_reactome.csv\n Name: rat_protein_reactions_reactome.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_protein_reactions_reactome.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.24/reviewed/rat_protein_reactions_reactome.csv" }