ArticleNucleic acids research2016
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers.
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133 citing papers in PubMed, 251 citations in OpenAlex.
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- ceQTL: a co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation.Briefings in bioinformatics · 2026Article
- Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry.Nature communications · 2025Article
- Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.Communications biology · 2025Article
- Unraveling the Role of MDK-SDC4 Interaction in Pancreatic Cancer-Associated New-Onset Diabetes by Single-Cell Transcriptomic Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Ultra-fast variant effect prediction using biophysical transcription factor binding models.Nucleic acids research · 2025Article
- Unraveling the intricate molecular landscape and potential biomarkers in lung adenocarcinoma through integrative epigenomic and transcriptomic profiling.Scientific reports · 2025Article
- Systematic functional characterization of non-coding regulatory SNPs associated with central obesity.American journal of human genetics · 2025Article
- Predicting CTCF cell type active binding sites in human genome.Scientific reports · 2024Article
- Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.bioRxiv : the preprint server for biology · 2024Article
- DNA methylation clocks for estimating biological age in Chinese cohorts.Protein & cell · 2024Article
- A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.Patterns (New York, N.Y.) · 2024Article
- HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.Nucleic acids research · 2024Article
- JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.Nucleic acids research · 2024Article
- CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq.Briefings in bioinformatics · 2023Article
- Enhancer variants on chromosome 2p14 regulating SPRED2 and ACTR2 act as a signal amplifier to protect against rheumatoid arthritis.American journal of human genetics · 2023Article
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- De novo human brain enhancers created by single-nucleotide mutations.Science advances · 2023Article
- Blimp-1 and c-Maf regulateWellcome open research · 2023Article
- Mechanisms underlying WNT-mediated priming of human embryonic stem cells.Development (Cambridge, England) · 2022Article
73 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Models of transcription factor (TF) binding sites provide a basis for a wide spectrum of studies in regulatory genomics, from reconstruction of regulatory networks to functional annotation of transcripts and sequence variants. While TFs may recognize different sequence patterns in different conditions, it is pragmatic to have a single generic model for each particular TF as a baseline for practical applications. Here we present the expanded and enhanced version of HOCOMOCO (http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco10), the collection of models of DNA patterns, recognized by transcription factors. HOCOMOCO now provides position weight matrix (PWM) models for binding sites of 601 human TFs and, in addition, PWMs for 396 mouse TFs. Furthermore, we introduce the largest up to date collection of dinucleotide PWM models for 86 (52) human (mouse) TFs. The update is based on the analysis of massive ChIP-Seq and HT-SELEX datasets, with the validation of the resulting models on in vivo data. To facilitate a practical application, all HOCOMOCO models are linked to gene and protein databases (Entrez Gene, HGNC, UniProt) and accompanied by precomputed score thresholds. Finally, we provide command-line tools for PWM and diPWM threshold estimation and motif finding in nucleotide sequences.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.