ArticleNucleic acids research2019
A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Search for Potential VDR/Partner Composite Elements in Regulatory DNA of Genes Associated with Respiratory Infections and Atopic Diseases.International journal of molecular sciences · 2025Article
- Article
- Asymmetry of Motif Conservation Within Their Homotypic Pairs Distinguishes DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data.International journal of molecular sciences · 2025Article
- Recent advances in designing synthetic plant regulatory modules.Frontiers in plant science · 2025Review
- A new pipeline SPICE identifies novel JUN-IKZF1 composite elements.bioRxiv : the preprint server for biology · 2024Article
- Analysis of auxin responses in the fern Ceratopteris richardii identifies the developmental phase as a major determinant for response properties.Development (Cambridge, England) · 2024Article
- Identification of transcription factor co-binding patterns with non-negative matrix factorization.Nucleic acids research · 2024Article
- Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data.NAR genomics and bioinformatics · 2024Article
- Sea-ATI unravels novel vocabularies of plant active cistrome.Nucleic acids research · 2023Article
- Transcription Factors as Important Regulators of Changes in Behavior through Domestication of Gray Rats: Quantitative Data from RNA Sequencing.International journal of molecular sciences · 2022Article
- Web-MCOT Server for Motif Co-Occurrence Search in ChIP-Seq Data.International journal of molecular sciences · 2022Article
- TF-COMB - Discovering grammar of transcription factor binding sites.Computational and structural biotechnology journal · 2022Article
- Motif models proposing independent and interdependent impacts of nucleotides are related to high and low affinity transcription factor binding sites in Arabidopsis.Frontiers in plant science · 2022Article
- Meta-Analysis of Transcriptome Data Detected New Potential Players in Response to Dioxin Exposure in Humans.International journal of molecular sciences · 2020Article
- Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome.BMC genetics · 2020Article
- Asymmetric Conservation within Pairs of Co-Occurred Motifs Mediates Weak Direct Binding of Transcription Factors in ChIP-Seq Data.International journal of molecular sciences · 2020Article
- Candidate SNP Markers of Atherogenesis Significantly Shifting the Affinity of TATA-Binding Protein for Human Gene Promoters show stabilizing Natural Selection as a Sum of Neutral Drift Accelerating Atherogenesis and Directional Natural Selection Slowing It.International journal of molecular sciences · 2020Article
- Motif grammar: The basis of the language of gene expression.Computational and structural biotechnology journal · 2020Review
- Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules.Frontiers in genetics · 2020Article
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8 authors.
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Abstract
Recognition of composite elements consisting of two transcription factor binding sites gets behind the studies of tissue-, stage- and condition-specific transcription. Genome-wide data on transcription factor binding generated with ChIP-seq method facilitate an identification of composite elements, but the existing bioinformatics tools either require ChIP-seq datasets for both partner transcription factors, or omit composite elements with motifs overlapping. Here we present an universal Motifs Co-Occurrence Tool (MCOT) that retrieves maximum information about overrepresented composite elements from a single ChIP-seq dataset. This includes homo- and heterotypic composite elements of four mutual orientations of motifs, separated with a spacer or overlapping, even if recognition of motifs within composite element requires various stringencies. Analysis of 52 ChIP-seq datasets for 18 human transcription factors confirmed that for over 60% of analyzed datasets and transcription factors predicted co-occurrence of motifs implied experimentally proven protein-protein interaction of respecting transcription factors. Analysis of 164 ChIP-seq datasets for 57 mammalian transcription factors showed that abundance of predicted composite elements with an overlap of motifs compared to those with a spacer more than doubled; and they had 1.5-fold increase of asymmetrical pairs of motifs with one more conservative 'leading' motif and another one 'guided'.
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