c-REDUCE: A Method for Detecting Motifs Related to Gene Expression
Author Information
Author(s): Kechris Katerina, Li Hao
Primary Institution: University of Colorado Denver
Hypothesis
Can incorporating sequence conservation improve the detection of motifs that correlate with gene expression?
Conclusion
Using sequence conservation information alongside correlation-based methods enhances the identification of known motifs.
Supporting Evidence
- c-REDUCE was tested on 78 genome-wide location datasets of 37 transcription factors.
- The method improved motif identification compared to other existing methods.
- c-REDUCE showed a correct prediction rate of ~65% for motifs not recovered by other programs.
Takeaway
The study created a new method called c-REDUCE that helps find important patterns in DNA by looking at similarities across different species.
Methodology
The method combines correlation-based motif finding with phylogenetic footprinting, evaluating orthologous sequences from multiple species.
Limitations
c-REDUCE may not effectively find very degenerate motifs or very long motifs due to sample size constraints.
Digital Object Identifier (DOI)
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