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HOCOMOCO specifications

Information


Unique identifier OMICS_00537
Name HOCOMOCO
Alternative name HOmo sapiens COmprehensive MOdel COllection
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 11.0
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline Ivan Kulakovskiy

Publications for HOmo sapiens COmprehensive MOdel COllection

HOCOMOCO citations

 (23)
library_books

Common α globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease

2018
PLoS Genet
PMCID: 5891078
PMID: 29590102
DOI: 10.1371/journal.pgen.1007293

[…] ENCODE project were used to search for DHS and transcription factor (TF) occupancy in blood-based tissues.[, ] TF binding motif disruptions were determined using the motifbreakR R package [] and the HOCOMOCO motif set.[] PhyloP calculations for 100 vertebrates were accessed using the University of California Santa Cruz (UCSC) genome browser []. MAZ, BACH1, TAL1, and MAFK knockdown using siRNAs an […]

library_books

SALP, a new single stranded DNA library preparation method especially useful for the high throughput characterization of chromatin openness states

2018
BMC Genomics
PMCID: 5811972
PMID: 29439663
DOI: 10.1186/s12864-018-4530-3

[…] nalysis was performed with PANTHER by uploading the genes to the website (http://pantherdb.org/) []. De novo motif analysis was performed with MEME tool and the comparison between enriched motifs and HOCOMOCO human v10 database was performed with Tomtom tool from MEME software suite [, ]. The BEDTools intersect was used to detect the overlapped peaks with –wa –u parameters []. All peak tracks were […]

library_books

THiCweed: fast, sensitive detection of sequence features by clustering big datasets

2017
Nucleic Acids Res
PMCID: 5861420
PMID: 29267972
DOI: 10.1093/nar/gkx1251

[…] cal motif lengths that one considers; here we used 50 bp. We compare the discovered motifs to previously reported motifs from JASPAR (,); the THiCweed website also includes comparisons to motifs from HocoMoco () and FactorBook (). […]

library_books

Genome wide dose dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super enhancers

2017
Nucleic Acids Res
PMCID: 5829637
PMID: 29240919
DOI: 10.1093/nar/gkx1225

[…] e MEME de novo motif finding algorithm. To identify related transcription factors, each identified motif was input to TOMTOM version 4.11.1 () using motif database JASPAR DNA CORE (2016) or HUMAN DNA HOCOMOCO (v10). We also report the E-value describing the certainty of the match between the identified de novo motif and the database position weight matrices. The images were prepared using Adobe Il […]

library_books

Systematic identification of regulatory variants associated with cancer risk

2017
Genome Biol
PMCID: 5651703
PMID: 29061142
DOI: 10.1186/s13059-017-1322-z

[…] The 500-bp SNP-containing regions were scanned using Fimo with human motif database HOCOMOCO v10 to predict TF binding [, ]. The predicted reference allele and alternative allele binding scores were calculated. Only those SNPs with either allele located in a predicted motif region an […]

library_books

Variation in DNA Damage Responses to an Inhalational Carcinogen (1,3 Butadiene) in Relation to Strain Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice

2017
Environ Health Perspect
PMCID: 5944832
PMID: 29038090
DOI: 10.1289/EHP1937

[…] t a background set of all accessible regions. Significant hits (E<0.05, where E represents a Bonferroni-corrected motif p-value) were selected, and these motifs were annotated using Tomtom () and the HOCOMOCO v. 10 database (http://hocomoco11.autosome.ru/) (). Proximal regions [<5 kb to the nearest transcription start site (TSS)] were analyzed separately from distal regions. […]

Citations

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HOCOMOCO institution(s)
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia; BIOSOFT.RU Ltd, Novosibirsk, Russia; Institute of Computational Technologies, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia; National Institute of Advanced Industrial Science and Technology (AIST), Com. Bio Big-Data Open Innovation Lab. (CBBD-OIL), AIST Tokyo Waterfront Main Bldg, Tokyo, Japan; King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
HOCOMOCO funding source(s)
Supported by Russian Science Foundation [17-74-10188]; King Abdullah University of Science and Technology (KAUST) [baseline fund BAS/1/1606- 01-01] and by the Skoltech Systems Biology Fellowship.

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