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.
 | |
| 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 |
Introduction
editTranscription 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
editRecognition
editAccording 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
editReferences
edit- ^ 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.