Finding Regulatory Elements in DNA
Author Information
Author(s): Jason Gertz, Justin C Fay, Barak A Cohen
Primary Institution: Washington University School of Medicine
Hypothesis
Can a new method that incorporates phylogenetic information improve the discovery of regulatory elements in DNA?
Conclusion
The experimental validation of a regulatory element prediction missed by other large-scale motif finding studies demonstrates that our approach is a useful addition to the current suite of tools for finding regulatory motifs.
Supporting Evidence
- The method achieved a sensitivity of 97% when applied to the Saccharomyces genomes.
- The study identified 218 hexamers that were significantly conserved, with 57% matching known binding sites.
- One experimentally validated motif was shown to activate gene expression in response to glucose.
Takeaway
Scientists created a new way to find important DNA sequences that control gene activity, and they proved it works by testing one of their predictions.
Methodology
The study developed a probabilistic framework that combines an HKY85 model with weight matrix models to assess genomic sequences for regulatory motifs.
Limitations
The method assumes perfect alignments at every evolutionary distance, which may not be realistic.
Statistical Information
P-Value
2.63 × 10-5
Statistical Significance
p<0.001
Digital Object Identifier (DOI)
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