HOCOMOCO explained

HOCOMOCO
Description:Curated collection of binding models for human and mouse transcription factors
Scope:Transcription factor binding profiles
Organism:Homo sapiens, Mus musculuslaboratory: autosome.orgauthor: Vorontsov, Makeev, Kulakovskiy
Citation:Vorontsov et al
Url: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 has been cited 396 times (as of January 2024). The publications have been cited 144 and 151 times.

See also

Notes and References

  1. 10.1093/nar/gkad1077. 0305-1048. 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. HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors. Nucleic Acids Research. 2023-11-16. 52. D1. D154–D163. 37971293. 10767914.
  2. 10.1093/nar/gkx1106. 1362-4962. 46. D1. 252–D259. 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.. HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Research. 2018-01-04. 29140464. 5753240.
  3. Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ . 6 . HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models . Nucleic Acids Research . 44 . D1 . D116–D125 . January 2016 . 26586801 . 4702883 . 10.1093/nar/gkv1249 .
  4. 10.1093/nar/gks1089. 1362-4962. 41. Database issue. 195–202. Kulakovskiy. Ivan V.. Medvedeva. Yulia A.. Schaefer. Ulf. Kasianov. Artem S.. Vorontsov. Ilya E.. Bajic. Vladimir B.. Makeev. Vsevolod J.. HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Research. 2013-01-01. 23175603. 3531053.
  5. 10.1016/j.gde.2017.02.007. 0959-437X. 43. 110–119. Inukai. Sachi. Kock. Kian Hong. Bulyk. Martha L. Transcription factor–DNA binding: beyond binding site motifs. Current Opinion in Genetics & Development. Genome architecture and expression. 2017-04-01. 28359978. 5447501.
  6. 10.1038/nrg1315. 1471-0064. 5. 4. 276–287. Wasserman. Wyeth W.. Sandelin. Albin. Applied bioinformatics for the identification of regulatory elements. Nature Reviews Genetics. April 2004. 15131651. 16599073.
  7. 10.1093/bioinformatics/16.1.16. 1367-4803. 16. 1. 16–23. Stormo. G. D.. DNA binding sites: representation and discovery. Bioinformatics. January 2000 . 10812473.

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