{
    "bcoid": "GLY_000320",
    "title": "Human Protein Reactions (Reactome)",
    "description": "The Human Protein Reactions (Reactome) dataset contains reactions information for pathways for Homo sapiens ...",
    "filename_list": "human_protein_reactions_reactome.csv",
    "filename": "human_protein_reactions_reactome.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Homo sapiens"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Reactions Reactome"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "pathway/enzymes"
        ]
    },
    "minitable": {
        "content": [
            [
                "R-HSA-903161...",
                "p-S133 CREB1..."
            ],
            [
                "R-HSA-903161...",
                "p-S133 CREB1..."
            ]
        ],
        "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-HSA-9031610",
                "p-S133 CREB1, MEF2D and SRF  bind the ARC gene",
                "nucleoplasm",
                "19116276",
                "R-HSA-9031628",
                "",
                "Activity-responsive transcription of the ARC gene is driven in part by a Synaptic Activity Response Element located ~7kb upstream of the transcription start site. This element is bound by CREB, SRF and MEF2D as assessed by EMSA and ChIP in mouse cells (Kawashima et al, 2009). SARE-driven ARC expression is responsive to stimulation through AMPAR and  NMDAR activity, and depends on CaMK and MAPK signaling pathways, consistent with previous studies (Kawashima et al, 2009; Falvell et al, 2006; Ramanan et al, 2005; Bourtchuladze et al, 1994; reviewed in Inoue et al, 2010; Finkbeiner et al, 1997; Epstein and Finkbeiner, 2018). Additional binding sites for SRF, MEF2D and ELK1 were also identified in another study, along with putative binding sites for an as-yet uncharacterized Zeste-like mammalian homologue (Pintchovski et al, 2006)."
            ],
            [
                "R-HSA-9031610",
                "p-S133 CREB1, MEF2D and SRF  bind the ARC gene",
                "nucleoplasm",
                "19193899",
                "R-HSA-9031628",
                "",
                "Activity-responsive transcription of the ARC gene is driven in part by a Synaptic Activity Response Element located ~7kb upstream of the transcription start site. This element is bound by CREB, SRF and MEF2D as assessed by EMSA and ChIP in mouse cells (Kawashima et al, 2009). SARE-driven ARC expression is responsive to stimulation through AMPAR and  NMDAR activity, and depends on CaMK and MAPK signaling pathways, consistent with previous studies (Kawashima et al, 2009; Falvell et al, 2006; Ramanan et al, 2005; Bourtchuladze et al, 1994; reviewed in Inoue et al, 2010; Finkbeiner et al, 1997; Epstein and Finkbeiner, 2018). Additional binding sites for SRF, MEF2D and ELK1 were also identified in another study, along with putative binding sites for an as-yet uncharacterized Zeste-like mammalian homologue (Pintchovski et al, 2006)."
            ]
        ]
    },
    "readme": "Name\n   - Human Protein Reactions (Reactome)\n\nVersion\n   - v-2.12.1\n\nCreated on\n  - 2019-11-30T15:06:36.890527\n\nModified on\n   - 2024-05-17T11:23:56.101Z\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@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 Human Protein Reactions (Reactome) dataset contains reactions information for pathways for Homo sapiens [taxid:9606] 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 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: all_blacklisted_pmids.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/all_blacklisted_pmids.csv\n      Name: human_protein_blacklisted_pmids_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/human_protein_blacklisted_pmids_uniprotkb.csv\n      Name: uniprot-proteome-homo-sapiens.nt\n      URI: https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-homo-sapiens.nt\n   Output Subdomain\n      Name: human_protein_reactions_reactome.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_reactions_reactome.csv\n      Name: human_protein_reactions_reactome.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_protein_reactions_reactome.stat.csv\n\nFields\n      Name: \"reaction_id\"\"\n     Description: \"\"\n      Unique Values: \"15177\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/human_protein_reactions_reactome.csv"
}