ArticleNucleic acids research2012
A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Multiomics Identification of Radioresistance-Associated Biomarkers and Prognostic Model Construction in Rectal Cancer.Human mutation · 2026Article
- Bioinformatics Approaches in Noncoding RNAs Research.Experientia supplementum (2012) · 2026Review
- Tomtom-lite: accelerating Tomtom enables large-scale and real-time motif similarity scoring.Bioinformatics (Oxford, England) · 2025Article
- Sequence-based prioritization of i-Motif candidates in the human genome.Frontiers in bioinformatics · 2025Article
- Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.International journal of molecular sciences · 2024Article
- Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models.Nucleic acids research · 2023Article
- Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication.Nature communications · 2023Article
- A survey on deep learning in DNA/RNA motif mining.Briefings in bioinformatics · 2021Article
- ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery.Bioinformatics (Oxford, England) · 2019Article
- Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production.Frontiers in bioengineering and biotechnology · 2018Review
- HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.Nucleic acids research · 2016Article
- Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells.Frontiers in genetics · 2016Review
- DiffLogo: a comparative visualization of sequence motifs.BMC bioinformatics · 2015Article
- De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.BMC genomics · 2014Article
- Article
- Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data.BMC genomics · 2014Article
- Article
- A general approach for discriminative de novo motif discovery from high-throughput data.Nucleic acids research · 2013Article
- Computational methodology for ChIP-seq analysis.Quantitative biology (Beijing, China) · 2013Article
- HOCOMOCO: a comprehensive collection of human transcription factor binding sites models.Nucleic acids research · 2013Article
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Authors and funding
6 authors.
Funding
Abstract
Identification of DNA motifs from ChIP-seq/ChIP-chip [chromatin immunoprecipitation (ChIP)] data is a powerful method for understanding the transcriptional regulatory network. However, most established methods are designed for small sample sizes and are inefficient for ChIP data. Here we propose a new k-mer occurrence model to reflect the fact that functional DNA k-mers often cluster around ChIP peak summits. With this model, we introduced a new measure to discover functional k-mers. Using simulation, we demonstrated that our method is more robust against noises in ChIP data than available methods. A novel word clustering method is also implemented to group similar k-mers into position weight matrices (PWMs). Our method was applied to a diverse set of ChIP experiments to demonstrate its high sensitivity and specificity. Importantly, our method is much faster than several other methods for large sample sizes. Thus, we have developed an efficient and effective motif discovery method for ChIP experiments.
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