{ "bcoid": "GLY_000319", "title": "Mouse Protein Reactions (Reactome)", "description": "The Mouse Protein Reactions (Reactome) dataset contains reactions information for pathways for mouse ...", "filename": "mouse_protein_reactions_reactome.csv", "filetype": "csv", "categories": { "species": "Mus Musculus", "molecule": "Protein", "tags": "Reactions Reactome", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "R-MMU-109514...", "TMP, (d)UMP,..." ], [ "R-MMU-109538...", "Concentrativ..." ] ], "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-MMU-109514", "TMP, (d)UMP, uridine 2' monophosphate, or uridine 3'-monophosphate + H2O => thymidine, deoxyuridine, or uridine + orthophosphate [NT5M]", "mitochondrial matrix", "", "R-MMU-73621" ], [ "R-MMU-109538", "Concentrative transport (import) of a nucleoside and two sodium ions by solute carrier family 28 (sodium-coupled nucleoside transporter), member 3", "mitochondrial matrix", "", "R-MMU-83936" ], [ "R-MMU-110011", "Binding of Grb10 to the insulin receptor", "mitochondrial matrix", "", "R-MMU-74749" ], [ "R-MMU-110322", "Formation of Pol zeta complex", "mitochondrial matrix", "", "R-MMU-110312" ], [ "R-MMU-111238", "Formation of ADAR2 homodimer", "mitochondrial matrix", "", "R-MMU-77042" ], [ "R-MMU-111742", "RNR (M1M2) reduces nucleotide diphosphates to deoxynucleotide diphosphates (glutaredoxin)", "mitochondrial matrix", "", "R-MMU-499943" ], [ "R-MMU-114542", "RAC1,RAC2,RHOG activate PI3K", "mitochondrial matrix", "", "R-MMU-1257604" ], [ "R-MMU-1183128", "PADIs:Ca2+ deiminate L-Arg to L-Cit in proteins", "mitochondrial matrix", "", "R-MMU-3247509" ], [ "R-MMU-1222491", "Lactoferrin scavenges iron ions", "mitochondrial matrix", "", "R-MMU-6799990" ], [ "R-MMU-1234181", "Nuclear PHD1,3 hydroxylates proline residues on HIF1A", "mitochondrial matrix", "", "R-MMU-1234176" ], [ "R-MMU-1247935", "OPLAH hydrolyses OPRO to L-Glu", "mitochondrial matrix", "", "R-MMU-174403" ], [ "R-MMU-1254285", "ERBB4s80:STAT5A complex translocates to the nucleus", "mitochondrial matrix", "", "R-MMU-1251985" ], [ "R-MMU-1254291", "ERBB4s80 binds STAT5A", "mitochondrial matrix", "", "R-MMU-1251985" ], [ "R-MMU-1306876", "NLRP3 activation by small molecules", "mitochondrial matrix", "", "R-MMU-844456" ], [ "R-MMU-1475414", "PTHP is reduced to BH4 by sepiapterin reductase (SPR)", "mitochondrial matrix", "", "R-MMU-1474151" ], [ "R-MMU-1482612", "2-acyl LPC is hydrolyzed to GPCho by PLA2[8]", "mitochondrial matrix", "", "R-MMU-1483115" ], [ "R-MMU-1482685", "1-acyl LPC is hydrolyzed to GPCho by PLA2[8]", "mitochondrial matrix", "", "R-MMU-1483115" ], [ "R-MMU-1497853", "Sepiapterin reductase (SPR) is phosphorylated by Ca2+/calmodulin-dependent protein kinase II", "mitochondrial matrix", "", "R-MMU-1474151" ], [ "R-MMU-1497869", "Salvage - Sepiapterin is reduced to BH2", "mitochondrial matrix", "", "R-MMU-1474151" ], [ "R-MMU-158721", "histidine-rich glycoprotein:plasminogen <-> histidine-rich glycoprotein + plasminogen", "mitochondrial matrix", "", "R-MMU-75205" ], [ "R-MMU-158722", "histidine-rich glycoprotein + plasminogen <-> histidine-rich glycoprotein:plasminogen", "mitochondrial matrix", "", "R-MMU-75205" ], [ "R-MMU-158941", "plasminogen + histidine-rich glycoprotein -> plasminogen:histidine-rich glycoprotein", "mitochondrial matrix", "", "R-MMU-75205" ], [ "R-MMU-1605591", "Glucosylceramidase cleaves the glucosidic bond of glucocerebroside to form ceramide", "mitochondrial matrix", "", "R-MMU-1660662" ], [ "R-MMU-1606273", "Sphingomyelin phosphodiesterase 2 and 3 (SMPD2 and 3) hydrolyse sphingomyelin to ceramide (plasma membrane)", "mitochondrial matrix", "", "R-MMU-1660662" ], [ "R-MMU-162683", "glucosaminyl-PI + fatty acyl-CoA -> glucosaminyl-acyl-PI + CoA-SH", "mitochondrial matrix", "", "R-MMU-162710" ], [ "R-MMU-162857", "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate", "mitochondrial matrix", "", "R-MMU-162710" ], [ "R-MMU-163090", "Elongation Of The Telomeric Chromosome End", "mitochondrial matrix", "", "R-MMU-171319" ], [ "R-MMU-163096", "Recruitment of Telomerase RNP to the Telomeric Chromosome End", "mitochondrial matrix", "", "R-MMU-171319" ], [ "R-MMU-163099", "Alignment Of The RNA Template On The Telomeric Chromosome End", "mitochondrial matrix", "", "R-MMU-171319" ], [ "R-MMU-163120", "Disassociation of Telomerase RNP and the Chromosome End", "mitochondrial matrix", "", "R-MMU-171319" ], [ "R-MMU-164617", "Elongation of Extended Telomeric Chromosome End", "mitochondrial matrix", "", "R-MMU-171319" ], [ "R-MMU-164620", "Translocation Of Telomerase RNP And Alignment Of RNA Template (TERC) To Extended Single Stranded Telomeric Chromosome-End", "mitochondrial matrix", "", "R-MMU-171319" ], [ "R-MMU-165726", "Phosphorylation of Ribosomal protein S6 by activated S6K1", "mitochondrial matrix", "", "R-MMU-166208" ], [ "R-MMU-1676114", "PI3P is dephosphorylated to PI by SACM1L at the Golgi membrane", "mitochondrial matrix", "", "R-MMU-1660514" ], [ "R-MMU-1676124", "PI4P is dephosphorylated to PI by SACM1L at the ER membrane", "mitochondrial matrix", "", "R-MMU-1483248" ], [ "R-MMU-1676133", "PI4P is dephosphorylated to PI by SACM1L at the Golgi membrane", "mitochondrial matrix", "", "R-MMU-1660514" ], [ "R-MMU-174439", "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere", "mitochondrial matrix", "", "R-MMU-174411" ], [ "R-MMU-174441", "Removal of RNA primer and dissociation of RPA and Dna2 from the C-strand", "mitochondrial matrix", "", "R-MMU-174437" ], [ "R-MMU-174447", "RFC dissociates after sliding clamp formation on the C-strand of the telomere", "mitochondrial matrix", "", "R-MMU-174411" ], [ "R-MMU-174451", "Recruitment of Dna2 endonuclease to the C strand", "mitochondrial matrix", "", "R-MMU-174437" ], [ "R-MMU-176059", "GST trimers transfer GS from GSH to luminal substrates", "mitochondrial matrix", "", "R-MMU-156590" ], [ "R-MMU-176101", "Recruitment of Rad17-RFC complex to DNA", "mitochondrial matrix", "", "R-MMU-176187" ], [ "R-MMU-176264", "Recruitment of the Rad9-Hus1-Rad1 complex to DNA", "mitochondrial matrix", "", "R-MMU-176187" ], [ "R-MMU-177784", "ribose 5-phosphate <=> D-ribulose 5-phosphate", "mitochondrial matrix", "", "R-MMU-71336" ], [ "R-MMU-192341", "Thiolysis of 3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-one-CoA yields choloyl-CoA (3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-one-CoA) and propionyl CoA", "mitochondrial matrix", "", "R-MMU-193368" ], [ "R-MMU-193533", "Thiolysis of 3alpha,7alpha-dihydroxy-5beta-cholan-24-one-CoA yields chenodeoxycholoyl-CoA (3alpha,7alpha-dihydroxy-5beta-cholan-24-one-CoA) and propionyl CoA", "mitochondrial matrix", "", "R-MMU-193368" ], [ "R-MMU-199206", "SLC5A6 cotransports extracellular PanK and 2Na+ to cytosol", "mitochondrial matrix", "", "R-MMU-199220" ], [ "R-MMU-199219", "SLC5A6 cotransports extracellular Btn and 2xNa+ to cytosol", "mitochondrial matrix", "", "R-MMU-196780" ], [ "R-MMU-200396", "Creatine transport across the plasma membrane", "mitochondrial matrix", "", "R-MMU-71288" ], [ "R-MMU-202203", "Recruitment of PI3K to plasma membrane", "mitochondrial matrix", "", "R-MMU-202424" ], [ "R-MMU-202365", "PI3K bound to TRAT1 phosphorylates PIP2 to PIP3", "mitochondrial matrix", "", "R-MMU-202424" ], [ "R-MMU-202713", "CD84 homodimerises", "mitochondrial matrix", "", "R-MMU-202733" ], [ "R-MMU-203797", "ERKs are inactivated by dual-specific phosphatases (DUSPs)", "mitochondrial matrix", "", "R-MMU-202670" ], [ "R-MMU-205136", "GTP-bound RAC contributes to JNK activation", "mitochondrial matrix", "", "R-MMU-193648" ], [ "R-MMU-205328", "Interaction of other tyrosine kinases with p-KIT", "mitochondrial matrix", "", "R-MMU-1433557" ], [ "R-MMU-2065357", "Prorenin:Prorenin Receptor hydrolyzes Angiotensinogen to Angiotensin-(1-10)", "mitochondrial matrix", "", "R-MMU-2022377" ], [ "R-MMU-2066781", "Formation of DHA-CoA catalysed by sterol carrier protein X (SCPx)", "mitochondrial matrix", "", "R-MMU-2046106" ], [ "R-MMU-209772", "Thyroxine is deiodinated to triiodothyronine", "mitochondrial matrix", "", "R-MMU-350864" ], [ "R-MMU-2130478", "Interaction of invariant chain trimer and MHC II alpha beta dimer", "mitochondrial matrix", "", "R-MMU-2132295" ], [ "R-MMU-2213241", "Formation of nonameric complex", "mitochondrial matrix", "", "R-MMU-2132295" ], [ "R-MMU-2247510", "MARCO:ligand is endocytosed", "mitochondrial matrix", "", "R-MMU-3000480" ], [ "R-MMU-2428930", "IGF1,2:p-Y1161,1165,1166-IGF1R binds IRS1,4", "mitochondrial matrix", "", "R-MMU-2428928" ], [ "R-MMU-2454113", "RBP3 transports 11cRAL to rod photoreceptor outer segment", "mitochondrial matrix", "", "R-MMU-2453902" ], [ "R-MMU-2464809", "RBP3 regulates the transport of atROL from ROS to RPE", "mitochondrial matrix", "", "R-MMU-2453902" ], [ "R-MMU-2465934", "11cROL translocates from Muller cells to cone photoreceptor cells", "mitochondrial matrix", "", "R-MMU-2187335" ], [ "R-MMU-2465938", "RBP3 regulates atROL taken up by Muller cells", "mitochondrial matrix", "", "R-MMU-2187335" ], [ "R-MMU-2467798", "PTTG1 (Securin) sequesters ESPL1 (Separase)", "mitochondrial matrix", "", "R-MMU-2467813" ], [ "R-MMU-2534096", "METAP1/2 demethylates GNAT1", "mitochondrial matrix", "", "R-MMU-2514859" ], [ "R-MMU-2562526", "PLK1 phosphorylates OPTN", "mitochondrial matrix", "", "R-MMU-2565942" ], [ "R-MMU-2584246", "GNAT1-GTP hydrolyses its bound GTP to GDP", "mitochondrial matrix", "", "R-MMU-2514859" ], [ "R-MMU-2685505", "TPCN1/2 transport lysosomal Ca2+ to cytosol ", "mitochondrial matrix", "", "R-MMU-2672351" ], [ "R-MMU-2872444", "SLC9B1/C2 exchange Na+ for H+", "mitochondrial matrix", "", "R-MMU-2672351" ], [ "R-MMU-3215251", "TP53INP1 and HIPK2 bind TP53", "mitochondrial matrix", "", "R-MMU-6804756" ], [ "R-MMU-3221982", "BANP binds TP53", "mitochondrial matrix", "", "R-MMU-6804759" ], [ "R-MMU-3222006", "STK11 (LKB1) phosphorylates NUAK1", "mitochondrial matrix", "", "R-MMU-6804756" ], [ "R-MMU-3222020", "NUAK1 phosphorylates TP53", "mitochondrial matrix", "", "R-MMU-6804756" ], [ "R-MMU-3222093", "BRD7 binds TP53 and EP300", "mitochondrial matrix", "", "R-MMU-6804758" ], [ "R-MMU-3222116", "L3MBTL1 binds TP53 monomethylated on K382", "mitochondrial matrix", "", "R-MMU-6804760" ], [ "R-MMU-3222128", "NOC2L binds TP53", "mitochondrial matrix", "", "R-MMU-6804756" ], [ "R-MMU-3222237", "SMYD2 methylates TP53", "mitochondrial matrix", "", "R-MMU-6804760" ], [ "R-MMU-3222259", "PHF20 binds TP53 dimethylated on K370 and K382", "mitochondrial matrix", "", "R-MMU-6804759" ], [ "R-MMU-3238999", "Activated human MKK3/MKK6 phosphorylates p38 MAPK complexed with MAPKAPK5", "mitochondrial matrix", "", "R-MMU-2559580" ], [ "R-MMU-3239014", "MAPKAPK5 phosphorylates TP53", "mitochondrial matrix", "", "R-MMU-2559580" ], [ "R-MMU-3239019", "Active p38 MAPK phosphorylates MAPKAPK5", "mitochondrial matrix", "", "R-MMU-2559580" ] ] }, "readme": "Name\n - Mouse Protein Reactions (Reactome)\n\nVersion\n - 1.5.11\n\nCreated on\n - 2019-11-30T15:03:14.488331\n\nModified on\n - 2019-12-04T12:04:31.501854\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 Reactions (Reactome) dataset contains reactions information for pathways for mouse [taxid:10090] 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/ln2wwwdata/source/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_reactions_reactome.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_reactions_reactome.csv\n Name: mouse_protein_reactions_reactome.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_reactions_reactome.stat.csv\n\nFields\n Name: \"reaction_id\"\n Description: \"\"\n Unique Values: \"7769\"\n Name: \"reaction_name\"\n Description: \"\"\n Unique Values: \"7747\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"4\"\n Name: \"pathway_id\"\n Description: \"\"\n Unique Values: \"1271\"\n Name: \"cellular_location\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.5.11/reviewed/mouse_protein_reactions_reactome.csv" }