Biology:HOCOMOCO
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| Content | |
| Description | Curated collection of binding models for human and mouse transcription factors |
| Data types captured | Transcription factor binding profiles |
| Organisms | Homo sapiens, Mus musculus
laboratory: autosome.org author: Vorontsov, Makeev, Kulakovskiy |
| Contact | |
| Primary citation | Vorontsov et al [1] |
| Access | |
| Website | HOCOMOCO |
HOCOMOCO[1][2] [3][4] is an open-access database providing curated and benchmarked binding motifs of human and mouse transcription factors. It captures the following data types: Homo sapiens (human) and Mus musculus (mouse) transcription factors, their DNA binding site motifs, and motif subtypes.
Introduction
Transcription factors (TFs) are proteins that bind DNA and thus regulate the trasncription process. The binding is sequence-specific. A sequence motif[5] is a model that describes the common pattern of the DNA binding sites[6] that a particular TF prefers to bind. One of the possible representations of the model is the Position-Weight Matrix (PWM)[7].
Organisms
- Homo sapiens
- Mus musculus
Recognition
According to the Web of Science, the 2018 publication of HOCOMOCO [2] has been cited 396 times (as of January 2024). The publications [3][4] have been cited 144 and 151 times.
See also
References
- ↑ 1.0 1.1 Vorontsov, Ilya E; Eliseeva, Irina A; Zinkevich, Arsenii; Nikonov, Mikhail; Abramov, Sergey; Boytsov, Alexandr; Kamenets, Vasily; Kasianova, Alexandra et al. (2023-11-16). "HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors". Nucleic Acids Research 52 (D1): D154–D163. doi:10.1093/nar/gkad1077. ISSN 0305-1048. PMID 37971293. PMC 10767914. https://doi.org/10.1093/nar/gkad1077.
- ↑ 2.0 2.1 Kulakovskiy, Ivan V.; Vorontsov, Ilya E.; Yevshin, Ivan S.; Sharipov, Ruslan N.; Fedorova, Alla D.; Rumynskiy, Eugene I.; Medvedeva, Yulia A.; Magana-Mora, Arturo et al. (2018-01-04). "HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis". Nucleic Acids Research 46 (D1): 252–D259. doi:10.1093/nar/gkx1106. ISSN 1362-4962. PMID 29140464.
- ↑ 3.0 3.1 "HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models". Nucleic Acids Research 44 (D1): D116–D125. January 2016. doi:10.1093/nar/gkv1249. PMID 26586801.
- ↑ 4.0 4.1 Kulakovskiy, Ivan V.; Medvedeva, Yulia A.; Schaefer, Ulf; Kasianov, Artem S.; Vorontsov, Ilya E.; Bajic, Vladimir B.; Makeev, Vsevolod J. (2013-01-01). "HOCOMOCO: a comprehensive collection of human transcription factor binding sites models". Nucleic Acids Research 41 (Database issue): 195–202. doi:10.1093/nar/gks1089. ISSN 1362-4962. PMID 23175603.
- ↑ Inukai, Sachi; Kock, Kian Hong; Bulyk, Martha L (2017-04-01). "Transcription factor–DNA binding: beyond binding site motifs". Current Opinion in Genetics & Development. Genome architecture and expression 43: 110–119. doi:10.1016/j.gde.2017.02.007. ISSN 0959-437X. PMID 28359978.
- ↑ Wasserman, Wyeth W.; Sandelin, Albin (April 2004). "Applied bioinformatics for the identification of regulatory elements". Nature Reviews Genetics 5 (4): 276–287. doi:10.1038/nrg1315. ISSN 1471-0064. PMID 15131651. https://www.nature.com/articles/nrg1315.
- ↑ Stormo, G. D. (January 2000). "DNA binding sites: representation and discovery". Bioinformatics (Oxford, England) 16 (1): 16–23. doi:10.1093/bioinformatics/16.1.16. ISSN 1367-4803. PMID 10812473.
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