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HOmo sapiens transcription factor COmprehensive MOdel COllection (HOCOMOCO): HOCOMOCO

IDNBDC common database IDs, which should be written in parentheses if there are multiple titles, such as Japanese and English. NBDC01690
Database nameName of the database HOmo sapiens transcription factor COmprehensive MOdel COllection (HOCOMOCO)
Alternative nameAlternative name of the database HOCOMOCO
URLURL of the database http://hocomoco.autosome.ru/
Database maintenance siteSite maintaining the database Institute of Systems Biology Ltd, KAUST (King Abdullah University of Science and Technology), Vavilov Institute of General Genetics, Russian Academy of Sciences
Country/RegionCountry or region name where the database maintenance site is located Russian Federation, Saudi Arabia
Database descriptionDatabase descirption 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) coveredNCBI Taxonomy names and IDs covered by the database Homo sapiens (9606), Mus musculus (10090)
Tag - TargetTag to indicate targets for this database such as genome and protein
Genome/Gene
cDNA/EST
Genetic variation
Epigenetics
DNA
RNA
Protein
Carbohydrate
Lipid
Metabolite
Chemical compound
Drug
Cell/Organelle
Organism
Health/Disease
Tag - Information typeTag to indicate information types for this database such as sequence and structure
Phenotype
Bioresource
Method
Ontology/Terminology/Nomenclature
Environment
Sequence
3D structure
Chemical structure
Expression
Localization
Geographic Distribution
Interaction/Pathway
Taxonomy
Classification
Image/Movie
Bibliography/Documents
Portal
Repository
Reference(s) - PubMed ID/DOIPubMed IDs/DOI for papers related to the database
PubMed ID:23175603
DOI:-
PubMed ID:26586801
DOI:-
PubMed ID:20736340
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PubMed ID:23427986
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PubMed ID:24074225
DOI:-
Language(s)Languages in which the contents of the database are displayed English
Operational statusOperational status for the database Active
Link(s) to Downloadable dataLinks to downloadable data ―
Link(s) to MetaData of downloadable dataLinks to metadata of downloadable data ―
Link(s) to Terms of useLinks to terms of use of downloadable data ―
Link(s) to "How to use" ―
Contact information of database ―
Link(s) to API / SPARQL endpoint ―
Link to LSDB ArchiveLink to LSDB Archive ―
Link to MEDALS Database listLink to MEDALS Database list ―
Link to TogoTVLink to TogoTV ―
Link to FAIRsharingLink to FAIRsharing https://fairsharing.org/10.25504/FAIRsharing.c1bjep
Similar databasesDatabases that are similar to this database.
Record maintainerRecord maintainer See the corresponding part in the FAIRsharing record
Record sourceOrganization that originally created the record
Date of creation of this recordDate of creation of this English record 2019-03-28
Last update date of this recordLast update date of this English record 2019-03-28
Record license Creative Commons Attribution and Share-alike (CC-BY-SA) International 4.0 license