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BMCBI
2008

c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression

9 years 12 months ago
c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression
Background: Computational methods for characterizing novel transcription factor binding sites search for sequence patterns or "motifs" that appear repeatedly in genomic regions of interest. Correlation-based motif finding strategies are used to identify motifs that correlate with expression data and do not rely on promoter sequences from a pre-determined set of genes. Results: In this work, we describe a method for predicting motifs that combines the correlationbased strategy with phylogenetic footprinting, where motifs are identified by evaluating orthologous sequence regions from multiple species. Our method, c-REDUCE, can account for variability at a motif position inferred from evolutionary information. c-REDUCE has been tested on ChIP-chip data for yeast transcription factors and on gene expression data in Drosophila. Conclusion: Our results indicate that utilizing sequence conservation information in addition to correlation-based methods improves the identification of ...
Katerina Kechris, Hao Li
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Katerina Kechris, Hao Li
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