{ "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-961590...", "AHCTF1 (ELYS..." ], [ "R-MMU-961837...", "POM121 binds..." ] ], "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-9615901", "AHCTF1 (ELYS) binds chromatin and Nup107-Nup160 complex", "plasma membrane", "", "R-MMU-9615933" ], [ "R-MMU-9618378", "POM121 binds the Nup107-Nup160 complex", "plasma membrane", "", "R-MMU-9615933" ], [ "R-MMU-9664855", "MAP1LC3B binds ATM dimer:Ub-p-PEX5:SQSTM1", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-9664880", "MAP1LC3B binds ATM dimer:Ub-p-PEX5:SQSTM1:NBR1", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-9664881", "NBR1 binds ATM:Ub-p-PEX5:SQSTM1", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-9664892", "SQSTM1 binds ATM dimer:Ub-p-PEX5", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-9674127", "USP30 deubiquitinates ATM dimer:Ub-p-PEX5", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-9674131", "USP30 binds ATM dimer:Ub-p-PEX5", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-9647977", "ICMT methylates S-Farn RAS proteins", "plasma membrane", "", "R-MMU-9648002" ], [ "R-MMU-9647978", "pro-RAS proteins are farnesylated", "plasma membrane", "", "R-MMU-9648002" ], [ "R-MMU-9647980", "mature RAS proteins translocate to plasma membrane", "plasma membrane", "", "R-MMU-9648002" ], [ "R-MMU-9647982", "S-farn Me-HRAS, -NRAS and -KRAS4A are palmitoylated", "plasma membrane", "", "R-MMU-9648002" ], [ "R-MMU-9647994", "RAS proteins are depalmitoylated", "plasma membrane", "", "R-MMU-9648002" ], [ "R-MMU-9647999", "RCE1 cleaves S-Farn proRAS proteins", "plasma membrane", "", "R-MMU-9648002" ], [ "R-MMU-9649733", "mature p21 RAS binds GDP", "plasma membrane", "", "R-MMU-9648002" ], [ "R-MMU-9649735", "Intrinsic nucleotide exchange on RAS", "plasma membrane", "", "R-MMU-5673001" ], [ "R-MMU-9649736", "RAS intrinsic GTPase activity hydrolyzes GTP to GDP", "plasma membrane", "", "R-MMU-5673001" ], [ "R-MMU-9660557", "RAS:GTP binds RAL GDS proteins", "plasma membrane", "", "R-MMU-5673001" ], [ "R-MMU-9667952", "ANKLE2 is deacetylated by SIRT2", "plasma membrane", "", "R-MMU-2995383" ], [ "R-MMU-9667965", "ANKLE2 binds PP2A", "plasma membrane", "", "R-MMU-2995383" ], [ "R-MMU-9668405", "SPAST (spastin) binds the IST1 subunit of ESCRT-III at the sites of microtubule attachment to chromatin", "plasma membrane", "", "R-MMU-9668328" ], [ "R-MMU-114256", "CYCS:APAF1 binds procaspase-9", "plasma membrane", "", "R-MMU-111458" ], [ "R-MMU-6797630", "LRPP4(LRPP1-3,5) hydrolyse LPA", "plasma membrane", "", "R-MMU-419408" ], [ "R-MMU-6804596", "APAF1:CYCS binds APIP", "plasma membrane", "", "R-MMU-9627069" ], [ "R-MMU-114254", "CYCS binds to APAF1", "plasma membrane", "", "R-MMU-111458" ], [ "R-MMU-3341294", "Superoxide reduces cytochrome c", "plasma membrane", "", "R-MMU-3299685" ], [ "R-MMU-9670673", "FIX is secreted", "plasma membrane", "", "R-MMU-140837" ], [ "R-MMU-9614271", "Autocleavage of ADGRG6", "plasma membrane", "", "R-MMU-9619665" ], [ "R-MMU-9614273", "ADGRG heterodimer translocates to plasma membrane", "plasma membrane", "", "R-MMU-9619665" ], [ "R-MMU-9664850", "ATM binds PEX5", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-9664862", "ATM dimer:PEX5 phosphorylates PEX5", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-9664879", "ATM:PEX5 binds ATM", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-9664883", "ATM:PEX5 translocates from cytosol to peroxisomal membrane", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-9664888", "ATM dimer:p-PEX5 ubiquitinates to form ATM dimer:Ub-p-PEX5", "plasma membrane", "", "R-MMU-9664873" ], [ "R-MMU-375768", "SLC7A2, isoform B (CAT-2B)-mediated uptake of cationic amino acids", "plasma membrane", "", "R-MMU-352230" ], [ "R-MMU-375790", "SLC7A2, isoform A (CAT-2A)-mediated uptake of cationic amino acids", "plasma membrane", "", "R-MMU-352230" ], [ "R-MMU-70870", "ECHS1 hydrates methacrylyl-CoA", "plasma membrane", "", "R-MMU-70895" ], [ "R-MMU-8944257", "Association of procollagen type XXIV", "plasma membrane", "", "R-MMU-8948216" ], [ "R-MMU-9650165", "ASIC trimers bind H+", "plasma membrane", "", "R-MMU-2672351" ], [ "R-MMU-9647746", "EML4 trimerizes", "plasma membrane", "", "R-MMU-9648025" ], [ "R-MMU-114252", "Cleavage of Procaspase-3 by the apoptosome", "plasma membrane", "", "R-MMU-111459" ], [ "R-MMU-114261", "Cleavage of Procaspase-7 by the apoptosome", "plasma membrane", "", "R-MMU-111459" ], [ "R-MMU-182594", "Association of INK4 family proteins with CDK4/6", "plasma membrane", "", "R-MMU-2559580" ], [ "R-MMU-3777129", "HDAC3 containing complexes deacetylate histone", "plasma membrane", "", "R-MMU-3214815" ], [ "R-MMU-5675206", "PEA15 binds MAPK monomers and dimers", "plasma membrane", "", "R-MMU-5673001" ], [ "R-MMU-9613213", "NAB2 and CHD4 bind and repress EGR-mediated RRAD gene expression", "plasma membrane", "", "R-MMU-9031628" ], [ "R-MMU-9627078", "XIAP binds CASP9", "plasma membrane", "", "R-MMU-9627069" ], [ "R-MMU-9627089", "CASP9 is phosphorylated at T125", "plasma membrane", "", "R-MMU-9627069" ], [ "R-MMU-9635739", "PTPN7 dephosphorylates p-T,Y-MAPKs", "plasma membrane", "", "R-MMU-5675221" ], [ "R-MMU-9635743", "PTPN7 binds p-T,Y-MAPK", "plasma membrane", "", "R-MMU-5675221" ], [ "R-MMU-9668597", "DNA polymerase:primase binds G-strand of the telomere", "plasma membrane", "", "R-MMU-174430" ], [ "R-MMU-9668831", "CST complex formation", "plasma membrane", "", "R-MMU-174430" ], [ "R-MMU-9674095", "PDGFRs bind type II TKI", "plasma membrane", "", "R-MMU-186797" ], [ "R-MMU-9686521", "CDK2:CCNA phosphorylates TERF2", "plasma membrane", "", "R-MMU-171319" ], [ "R-MMU-9686524", "PP6-PPP6R3 dephosphorylates TERF2", "plasma membrane", "", "R-MMU-171319" ], [ "R-MMU-1006143", "CD46 binds C3b", "plasma membrane", "", "R-MMU-977606" ], [ "R-MMU-1008200", "NFE2 binds the beta globin locus control region", "plasma membrane", "", "R-MMU-983231" ], [ "R-MMU-1008248", "Adenylate Kinase 3 is a GTP-AMP phosphotransferase", "plasma membrane", "", "R-MMU-983231" ], [ "R-MMU-1011576", "EHD proteins interact with Rabenosyn-5", "plasma membrane", "", "R-MMU-983231" ], [ "R-MMU-1011598", "DOCKs bind to RhoGEFs", "plasma membrane", "", "R-MMU-983231" ], [ "R-MMU-1011600", "Rabenosyn-5 connects Rab5 to VPS-45", "plasma membrane", "", "R-MMU-983231" ], [ "R-MMU-1022127", "Ub-unfolded protein:(GlcNAc)2 (Man)9-5 translocates from ERQC to cytosol", "plasma membrane", "", "R-MMU-901032" ], [ "R-MMU-1067640", "IL6 binds IL6R-2", "plasma membrane", "", "R-MMU-1059683" ], [ "R-MMU-1067651", "IL6:IL6R-2 binds IL6ST:JAK1, JAK2, (TYK2)", "plasma membrane", "", "R-MMU-1059683" ], [ "R-MMU-1067659", "Assembly of hexameric IL-6 receptor", "plasma membrane", "", "R-MMU-1059683" ], [ "R-MMU-1067667", "IL6 binds IL6R", "plasma membrane", "", "R-MMU-1059683" ], [ "R-MMU-1067676", "IL6:IL6R-2 binds IL6ST-2", "plasma membrane", "", "R-MMU-1059683" ], [ "R-MMU-1067688", "IL6:IL6R binds IL6ST:JAK1,JAK2,(TYK2)", "plasma membrane", "", "R-MMU-1059683" ], [ "R-MMU-109636", "Recognition and Binding of Core Promoter Elements by TFIID", "plasma membrane", "", "R-MMU-73779" ], [ "R-MMU-109637", "Binding of TFIIA and TFIIB to the pol II promoter:TFIID complex", "plasma membrane", "", "R-MMU-73779" ], [ "R-MMU-109638", "Recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB complex", "plasma membrane", "", "R-MMU-73779" ], [ "R-MMU-109639", "Formation of the closed pre-initiation complex", "plasma membrane", "", "R-MMU-73779" ], [ "R-MMU-109699", "PI3K-containing complexes phosphorylate PIP2 to PIP3", "plasma membrane", "", "R-MMU-109704" ], [ "R-MMU-109700", "AKT2 binds PIP3", "plasma membrane", "", "R-MMU-165158" ], [ "R-MMU-109701", "PDPK1 binds PIP3", "plasma membrane", "", "R-MMU-165158" ], [ "R-MMU-109702", "PDPK1 phosphorylates AKT2", "plasma membrane", "", "R-MMU-165158" ], [ "R-MMU-109813", "GRB2-1 binds SOS1", "plasma membrane", "", "R-MMU-179812" ], [ "R-MMU-109955", "Formation of ERCC1:XPF heterodimeric complex", "plasma membrane", "", "R-MMU-5696395" ], [ "R-MMU-110133", "(d)GDP + ADP <=> (d)GMP + ATP (GUK1)", "plasma membrane", "", "R-MMU-499943" ], [ "R-MMU-110137", "(d)ADP or (d)CDP + ADP <=> (d)AMP or (d)CMP + ATP", "plasma membrane", "", "R-MMU-499943" ], [ "R-MMU-110138", "AK5,7,8,9 phosphorylates (d)NMPs to (d)NDPs", "plasma membrane", "", "R-MMU-499943" ], [ "R-MMU-110141", "(d)ADP + ADP <=> (d)AMP + ATP (AK1)", "plasma membrane", "", "R-MMU-499943" ], [ "R-MMU-110144", "ADP + ADP <=> AMP + ATP [AK2]", "plasma membrane", "", "R-MMU-499943" ], [ "R-MMU-110145", "AMP + ATP <=> ADP + ADP [AK2]", "plasma membrane", "", "R-MMU-499943" ] ] }, "readme": "Name\n - Mouse Protein Reactions (Reactome)\n\nVersion\n - 1.8.25\n\nCreated on\n - 2019-11-30T15:03:14.488331\n\nModified on\n - 2020-04-10T12:48:04.969443\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: \"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-1.8.25/reviewed/mouse_protein_reactions_reactome.csv" }