HOmo sapiens transcription factor COmprehensive MOdel COllection (HOCOMOCO): HOCOMOCO
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| Database maintenance site: | Institute of Systems Biology Ltd, KAUST (King Abdullah University of Science and Technology), Vavilov Institute of General Genetics, Russian Academy of Sciences |
| Country/Region: | Russian Federation, Saudi Arabia |
| Database description: | HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) v10 provides transcription factor (TF) binding models for 601 human and 396 mouse TFs. In addition to basic mononucleotide position weight matrices (PWMs), HOCOMOCO provides a set of dinucleotide position weight matrices based on ChIP-Seq data. All the models were produced by the ChIPMunk motif discovery tool. Models are manually curated with assigning model quality ratings based upon benchmark studies or inherited from HOCOMOCO v9. ChIP-Seq data for motif discovery was extracted from GTRD database of BioUML platform, that also provides an interface for motif finding (sequence scanning) with HOCOMOCO models. Other sequences of TF binding DNA regions were collected from existing databases and other public data. An appropriate TFBS model was selected for each TF, with similar models selected for related TFs. All TFBS models and initial binding segments data used for motif discovery were mapped to UniPROT IDs. TF coding genes are linked with GeneCards entries. DNA binding domains are linked with TF class database. |
| Organism(s) covered: | , |
| Tag - Target: | Protein, Genome/Gene |
| Tag - Information type: | Interaction/Pathway |
| Reference(s) - PubMed ID/DOI: | PubMed ID: DOI: PubMed ID: DOI: PubMed ID: DOI: PubMed ID: DOI: PubMed ID: DOI: |
| Language(s): | English |
| Operational status: | Active |
| Link(s) to Downloadable data: | - |
| Link(s) to Metadata of downloadable data: | - |
| Link(s) to Terms of use: | - |
| Link(s) to "How to use": | - |
| Contact information of database: | - |
| Link(s) to API / SPARQL endpoint | - |
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Link to LSDB Archive:
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Link to MEDALS Database list:
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Link to TogoTV:
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Link to FAIRsharing:
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https://fairsharing.org/10.25504/FAIRsharing.c1bjep |
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Similar databases:
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ChIP-Atlas PINT MAPPER-2 Plant Transcription Factor Database PTM-Switchboard ReMap SPAD LinkProt: A database of proteins with topological links Interologous Interaction Database PRofils pour l'Identification Automatique du Metabolisme |
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Record maintainer
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See the corresponding part in the FAIRsharing record. |
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Record source:
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 (2018-12-21)
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Date of creation of this record:
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2019-03-28 |
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Last update date of this record:
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2019-03-28 |
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Record license:
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Creative Commons Attribution and Share-alike (CC-BY-SA) International 4.0 license |