HOCOMOCO
 | |
| 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
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
- ^ a b Vorontsov, Ilya E; Eliseeva, Irina A; Zinkevich, Arsenii; Nikonov, Mikhail; Abramov, Sergey; Boytsov, Alexandr; Kamenets, Vasily; Kasianova, Alexandra; Kolmykov, Semyon; Yevshin, Ivan S; Favorov, Alexander; Medvedeva, Yulia A; Jolma, Arttu; Kolpakov, Fedor; Makeev, Vsevolod J; Kulakovskiy, Ivan V (16 November 2023). "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. PMC 10767914. PMID 37971293.
- ^ a b Kulakovskiy, Ivan V.; Vorontsov, Ilya E.; Yevshin, Ivan S.; Sharipov, Ruslan N.; Fedorova, Alla D.; Rumynskiy, Eugene I.; Medvedeva, Yulia A.; Magana-Mora, Arturo; Bajic, Vladimir B.; Papatsenko, Dmitry A.; Kolpakov, Fedor A.; Makeev, Vsevolod J. (4 January 2018). "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. PMC 5753240. PMID 29140464.
- ^ a b Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, et al. (January 2016). "HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models". Nucleic Acids Research. 44 (D1): D116–D125. doi:10.1093/nar/gkv1249. PMC 4702883. PMID 26586801.
- ^ a b Kulakovskiy, Ivan V.; Medvedeva, Yulia A.; Schaefer, Ulf; Kasianov, Artem S.; Vorontsov, Ilya E.; Bajic, Vladimir B.; Makeev, Vsevolod J. (1 January 2013). "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. PMC 3531053. PMID 23175603.
- ^ Inukai, Sachi; Kock, Kian Hong; Bulyk, Martha L (1 April 2017). "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. PMC 5447501. 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. S2CID 16599073.
- ^ Stormo, G. D. (January 2000). "DNA binding sites: representation and discovery". Bioinformatics. 16 (1): 16–23. doi:10.1093/bioinformatics/16.1.16. ISSN 1367-4803. PMID 10812473.