HOCOMOCO
{{Short description|Database of human and mouse transcription factor binding sites}}
{{Use dmy dates|date=January 2024}}
{{infobox biodatabase
|title = HOCOMOCO
|logo =File:Database.png
|description = Curated collection of binding models for human and mouse transcription factors
|scope = Transcription factor binding profiles
|organism = Homo sapiens, Mus musculus
laboratory: [https://autosome.org/ autosome.org]
author: Vorontsov, Makeev, Kulakovskiy
|url = [https://hocomoco.autosome.org/ HOCOMOCO]
}}
HOCOMOCO{{Cite journal| doi = 10.1093/nar/gkad1077| issn = 0305-1048| last1 = Vorontsov| first1 = Ilya E| last2 = Eliseeva| first2 = Irina A| last3 = Zinkevich| first3 = Arsenii| last4 = Nikonov| first4 = Mikhail| last5 = Abramov| first5 = Sergey| last6 = Boytsov| first6 = Alexandr| last7 = Kamenets| first7 = Vasily| last8 = Kasianova| first8 = Alexandra| last9 = Kolmykov| first9 = Semyon| last10 = Yevshin| first10 = Ivan S| last11 = Favorov| first11 = Alexander| last12 = Medvedeva| first12 = Yulia A| last13 = Jolma| first13 = Arttu| last14 = Kolpakov| first14 = Fedor| last15 = Makeev| first15 = Vsevolod J| last16 = Kulakovskiy| first16 = Ivan V| title = HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors| journal = Nucleic Acids Research| date = 2023-11-16| volume = 52| issue = D1| pages = D154–D163| pmid = 37971293| pmc = 10767914| url = https://doi.org/10.1093/nar/gkad1077}}{{Cite journal| doi = 10.1093/nar/gkx1106| issn = 1362-4962| volume = 46| issue = D1| pages = 252–D259| last1 = Kulakovskiy| first1 = Ivan V.| last2 = Vorontsov| first2 = Ilya E.| last3 = Yevshin| first3 = Ivan S.| last4 = Sharipov| first4 = Ruslan N.| last5 = Fedorova| first5 = Alla D.| last6 = Rumynskiy| first6 = Eugene I.| last7 = Medvedeva| first7 = Yulia A.| last8 = Magana-Mora| first8 = Arturo| last9 = Bajic| first9 = Vladimir B.| last10 = Papatsenko| first10 = Dmitry A.| last11 = Kolpakov| first11 = Fedor A.| last12 = Makeev| first12 = Vsevolod J.| title = HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis| journal = Nucleic Acids Research| date = 2018-01-04| pmid = 29140464| pmc = 5753240}}
{{cite journal | vauthors = Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ | display-authors = 6 | title = HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models | journal = Nucleic Acids Research | volume = 44 | issue = D1 | pages = D116–D125 | date = January 2016 | pmid = 26586801 | pmc = 4702883 | doi = 10.1093/nar/gkv1249 }}{{Cite journal| doi = 10.1093/nar/gks1089| issn = 1362-4962| volume = 41| issue = Database issue| pages = 195–202| last1 = Kulakovskiy| first1 = Ivan V.| last2 = Medvedeva| first2 = Yulia A.| last3 = Schaefer| first3 = Ulf| last4 = Kasianov| first4 = Artem S.| last5 = Vorontsov| first5 = Ilya E.| last6 = Bajic| first6 = Vladimir B.| last7 = Makeev| first7 = Vsevolod J.| title = HOCOMOCO: a comprehensive collection of human transcription factor binding sites models| journal = Nucleic Acids Research| date = 2013-01-01| pmid = 23175603| pmc = 3531053}} 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 transcription process. The binding is sequence-specific. A sequence motif{{Cite journal| doi = 10.1016/j.gde.2017.02.007| issn = 0959-437X| volume = 43| pages = 110–119| last1 = Inukai| first1 = Sachi| last2 = Kock| first2 = Kian Hong| last3 = Bulyk| first3 = Martha L| title = Transcription factor–DNA binding: beyond binding site motifs| journal = Current Opinion in Genetics & Development| series = Genome architecture and expression| date = 2017-04-01| pmid = 28359978| pmc = 5447501}} is a model that describes the common pattern of the DNA binding sites{{Cite journal| doi = 10.1038/nrg1315| issn = 1471-0064| volume = 5| issue = 4| pages = 276–287| last1 = Wasserman| first1 = Wyeth W.| last2 = Sandelin| first2 = Albin| title = Applied bioinformatics for the identification of regulatory elements| journal = Nature Reviews Genetics| date = April 2004| pmid = 15131651| s2cid = 16599073| url = https://www.nature.com/articles/nrg1315| url-access = subscription}} that a particular TF prefers to bind. One of the possible representations of the model is the Position-Weight Matrix (PWM).{{Cite journal| doi = 10.1093/bioinformatics/16.1.16| issn = 1367-4803| volume = 16| issue = 1| pages = 16–23| last = Stormo| first = G. D.| title = DNA binding sites: representation and discovery| journal = Bioinformatics| date = January 2000 | pmid = 10812473}}
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.