ArticleNature biotechnology2002
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.
Article in Nature biotechnology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 284 papers.
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Who cites it
284 citing papers in PubMed.
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- A survey on algorithms to characterize transcription factor binding sites.Briefings in bioinformatics · 2023Review
- Biogenesis of telomerase RNA from a protein-coding mRNA precursor.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor.Scientific reports · 2022Article
- PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.Methods in molecular biology (Clifton, N.J.) · 2022Article
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- Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1.Scientific reports · 2020Article
- Set cover-based methods for motif selection.Bioinformatics (Oxford, England) · 2020Article
- SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.Bioinformatics (Oxford, England) · 2019Article
- Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.Molecular cell · 2019Article
- Defining the binding determinants ofThe Journal of biological chemistry · 2018Article
- Dempster-Shafer Theory for the Prediction of Auxin-Response Elements (AuxREs) in Plant Genomes.BioMed research international · 2018Article
- Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape.Bioinformatics (Oxford, England) · 2017Article
- Noncoding Variants Functional Prioritization Methods Based on Predicted Regulatory Factor Binding Sites.Current genomics · 2017Review
- Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
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- Predictive Models of Spatial Transcriptional Response to High Salinity.Plant physiology · 2017Article
224 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-array) has become a popular procedure for studying genome-wide protein-DNA interactions and transcription regulation. However, it can only map the probable protein-DNA interaction loci within 1-2 kilobases resolution. To pinpoint interaction sites down to the base-pair level, we introduce a computational method, Motif Discovery scan (MDscan), that examines the ChIP-array-selected sequences and searches for DNA sequence motifs representing the protein-DNA interaction sites. MDscan combines the advantages of two widely adopted motif search strategies, word enumeration and position-specific weight matrix updating, and incorporates the ChIP-array ranking information to accelerate searches and enhance their success rates. MDscan correctly identified all the experimentally verified motifs from published ChIP-array experiments in yeast (STE12, GAL4, RAP1, SCB, MCB, MCM1, SFF, and SWI5), and predicted two motif patterns for the differential binding of Rap1 protein in telomere regions. In our studies, the method was faster and more accurate than several established motif-finding algorithms. MDscan can be used to find DNA motifs not only in ChIP-array experiments but also in other experiments in which a subgroup of the sequences can be inferred to contain relatively abundant motif sites. The MDscan web server can be accessed at http://BioProspector.stanford.edu/MDscan/.
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