{ "bcoid": "GLY_000769", "title": "Yeast Protein Reactions (Reactome)", "description": "The Yeast Protein Reactions (Reactome) dataset contains reactions information for pathways for yeast ...", "filename": "yeast_protein_reactions_reactome.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Reactions Reactome" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "R-SCE-101159...", "DOCKs bind t..." ], [ "R-SCE-109636...", "Recognition ..." ] ], "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" }, { "type": "string", "label": "equation" }, { "type": "string", "label": "reaction_summary" } ], [ "R-SCE-1011598", "DOCKs bind to RhoGEFs", "", "", "", "", "" ], [ "R-SCE-109636", "Recognition and Binding of Core Promoter Elements by TFIID", "", "", "", "", "" ], [ "R-SCE-109637", "Binding of TFIIA and TFIIB to the pol II promoter:TFIID complex", "", "", "", "", "" ], [ "R-SCE-109638", "Recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB complex", "", "", "", "", "" ], [ "R-SCE-109639", "Formation of the closed pre-initiation complex", "", "", "", "", "" ], [ "R-SCE-109702", "PDPK1 phosphorylates AKT2", "", "", "", "", "" ], [ "R-SCE-109857", "MAP2K1 binds MAPK3", "", "", "", "", "" ], [ "R-SCE-109858", "MAP2K2 binds MAPK1", "", "", "", "", "" ], [ "R-SCE-109860", "MAP2K1 phosphorylates MAPK3", "", "", "", "", "" ], [ "R-SCE-109862", "MAP2K2 phosphorylates MAPK1", "", "", "", "", "" ], [ "R-SCE-109863", "Dissociation of p-T,Y-MAPK3:MAP2K1", "", "", "", "", "" ], [ "R-SCE-109864", "Dissociation of p-T,Y-MAPK1:p-S,T-MAP2K2", "", "", "", "", "" ], [ "R-SCE-110144", "ADP + ADP <=> AMP + ATP [AK2]", "", "", "", "", "" ], [ "R-SCE-110145", "AMP + ATP <=> ADP + ADP [AK2]", "", "", "", "", "" ], [ "R-SCE-110322", "Formation of Pol zeta complex", "", "", "", "", "" ], [ "R-SCE-111264", "Addition of nucleotides between position +11 and +30", "", "", "", "", "" ], [ "R-SCE-111849", "RNA Polymerase III Promoter Opening", "", "1619662", "", "", "" ], [ "R-SCE-111879", "PIP2 hydrolysis", "", "", "", "", "" ], [ "R-SCE-111898", "Phosphorylation of cPLA2 by ERK-2", "", "", "", "", "" ], [ "R-SCE-111925", "cAMP induces dissociation of inactive PKA tetramers", "", "", "", "", "" ], [ "R-SCE-111942", "RNA Polymerase III Initiation At a Simple Start Sequence", "", "7659514", "", "", "" ], [ "R-SCE-111943", "RNA Polymerase III Abortive Initiation", "", "10473618", "", "", "" ], [ "R-SCE-111945", "Beginning of RNA Polymerase III Productive Transcription", "", "8308883", "", "", "" ], [ "R-SCE-111946", "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites", "", "9278445", "", "", "" ], [ "R-SCE-112037", "Inactivation of PLC beta", "", "", "", "", "" ], [ "R-SCE-112383", "Hypophosphorylation of RNA Pol II CTD by FCP1P protein", "", "", "", "", "" ], [ "R-SCE-112434", "Formation of DSIF complex ", "", "", "", "", "" ], [ "R-SCE-112466", "RNA Polymerase III Transcriptional Pause at Terminator Sequence", "", "8308883", "", "", "" ], [ "R-SCE-112480", "RNA Polymerase III Termination and release of transcribed RNA", "", "11118217", "", "", "" ], [ "R-SCE-112480", "RNA Polymerase III Termination and release of transcribed RNA", "", " 8035818", "", "", "" ], [ "R-SCE-112480", "RNA Polymerase III Termination and release of transcribed RNA", "", " 8308883", "", "", "" ], [ "R-SCE-112480", "RNA Polymerase III Termination and release of transcribed RNA", "", " 9660958", "", "", "" ], [ "R-SCE-113407", "DSIF complex binds to RNA Pol II (hypophosphorylated)", "", "", "", "", "" ], [ "R-SCE-113409", "Abortive termination of early transcription elongation by DSIF:NELF", "", "", "", "", "" ], [ "R-SCE-113430", "Extrusion of 5'-end of 30 nt long transcript through the pore in Pol II complex", "", "", "", "", "" ], [ "R-SCE-113504", "Detection of damage during initiation of DNA synthesis in S-phase", "", "", "", "", "" ], [ "R-SCE-114284", "Release of Cytochrome c from mitochondria", "", "", "", "", "" ], [ "R-SCE-114553", "Activation of conventional Protein Kinase C", "", "", "", "", "" ], [ "R-SCE-114683", "Phosphorylation of Platelet Sec-1", "", "", "", "", "" ], [ "R-SCE-114684", "Phosphorylation of Syntaxin-4", "", "", "", "", "" ], [ "R-SCE-114688", "PLC-beta hydrolyses PIP2 to DAG and IP3", "", "", "", "", "" ], [ "R-SCE-1168373", "PRKCB (Protein kinase C beta, PKC-beta) binds diacylglycerol and phosphatidylserine", "", "", "", "", "" ], [ "R-SCE-1236970", "Proteasomal clevage of exogenous antigen", "", "", "", "", "" ], [ "R-SCE-1247960", "Activation of p38 MAPK", "", "", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", "10397776", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 10469659", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 11344168", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 12574118", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 1350514", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 17074805", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 17148445", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 17828250", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 18070913", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 19139266", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 19144822", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 19884344", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 9312000", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 15797382", "", "", "" ], [ "R-SCE-1252249", "TIM23 SORT complex inserts proteins into inner membrane", "", " 18418384", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", "18678864", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 10779357", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 16107694", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 14638855", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 16790493", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 10367886", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 11344168", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 12574118", "", "", "" ], [ 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"TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 7798311", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 7809127", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 7935837", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 7973708", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 8408191", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 8654364", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 14981507", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 15797382", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 16105940", "", "", "" ], [ "R-SCE-1252253", "TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix", "", " 18418384", "", "", "" ], [ "R-SCE-1252255", "TOM40:TOM70 complex translocates proteins from the cytosol to the mitochondrial intermembrane space", "", "19767391", "", "", "" ] ] }, "readme": "Name\n - Yeast Protein Reactions (Reactome)\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2022-09-06T11:25:28.437609\n\nModified on\n - 2023-09-11T19:20:20\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@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 Yeast Protein Reactions (Reactome) dataset contains reactions information for pathways for yeast [taxid:559292] UniProtKB accessions that includes reaction participants, pathway ID, reaction ID, PMID etc from Reactome database. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB, Reactome 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/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-saccharomyces-cerevisiae.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_10_30/uniprot-proteome-saccharomyces-cerevisiae.nt\n Output Subdomain\n Name: yeast_protein_reactions_reactome.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_reactions_reactome.csv\n Name: yeast_protein_reactions_reactome.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_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: \"1571\"\n Name: \"reaction_name\"\n Description: \"The name assigned to a reaction in Reactome database\"\n Unique Values: \"1569\"\n Name: \"cellular_location\"\n Description: \"The loaction in the cell where reaction occurs\"\n Unique Values: \"1\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"248\"\n Name: \"pathway_id\"\n Description: \"Pathway Identifier\"\n Unique Values: \"1\"\n Name: \"equation\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"reaction_summary\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/yeast_protein_reactions_reactome.csv" }