{
    "bcoid": "GLY_000750",
    "title": "Yeast Protein Function (UniProtKB)",
    "description": "The Yeast Protein Function (UniProtKB) dataset contains biological function annotation for Saccharomyces ...",
    "filename_list": "yeast_protein_function_uniprotkb.csv",
    "filename": "yeast_protein_function_uniprotkb.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Saccharomyces cerevisiae S288C"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Protein Function"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ]
    },
    "minitable": {
        "content": [
            [
                "Q03761-1...",
                "protein_xref..."
            ],
            [
                "Q03761-1...",
                "protein_xref..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "xref_key..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "xref_key"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "annotation"
                }
            ],
            [
                "Q03761-1",
                "protein_xref_uniprotkb_fun",
                "Q03761",
                "Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus."
            ],
            [
                "Q03761-1",
                "protein_xref_pubmed",
                "10788514",
                "Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus."
            ]
        ]
    },
    "readme": "Name\n   - Yeast Protein Function (UniProtKB)\n\nVersion\n   - v-2.9.1\n\nCreated on\n  - 2022-08-30T14:58:43.098400\n\nModified on\n   - 2025-03-04T16:59:16.158Z\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], 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 Yeast Protein Function (UniProtKB) dataset contains biological function annotation for Saccharomyces cerevisiae S288C [taxid:559292] protein accessions from the UniProtKB database. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n\nDescription Domain\n   Keywords\n   - protein function\n   - UniProtKB\n\n   Pipeline Steps\n   - Step-1: The script loads the UniProtKB function annotations triplestore containing triples from nt file and extracts the data as a csv dataset. \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/2025_05_20/uniprot-proteome-saccharomyces-cerevisiae.nt\n   Output Subdomain\n      Name: yeast_protein_function_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/yeast_protein_function_uniprotkb.csv\n      Name: yeast_protein_function_uniprotkb.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/yeast_protein_function_uniprotkb.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"\"\n      Unique Values: \"4879\"\n      Name: \"xref_key\"\n     Description: \"Source key associated to the  xref_id\"\n      Unique Values: \"3\"\n      Name: \"xref_id\"\n     Description: \"ID of the X-ref\"\n      Unique Values: \"12414\"\n      Name: \"annotation\"\n     Description: \"Function annotation from UniProtKB|RefSeq database\"\n      Unique Values: \"4095\"",
    "downloadurl": "/ln2data/releases/data/v-2.9.1/reviewed/yeast_protein_function_uniprotkb.csv"
}