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Related Experiment Videos

Sampling motifs on phylogenetic trees.

Xiaoman Li1, Wing H Wong

  • 1Department of Statistics, Stanford University, Sequoia Hall, 390 Serra Mall, Stanford, CA 94305-4065, USA. shawnli@stanford.edu

Proceedings of the National Academy of Sciences of the United States of America
|June 29, 2005
PubMed
Summary
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We developed a novel computational method to identify regulatory DNA motifs by combining overrepresentation and evolutionary conservation. This approach improves motif discovery accuracy, even in distantly related species, advancing genomic analysis.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying regulatory DNA motifs is crucial for understanding gene regulation.
  • Current motif discovery methods struggle with divergent species due to unreliable sequence alignments.
  • Evolutionary conservation and overrepresentation are key properties of functional motifs.

Purpose of the Study:

  • To develop a novel computational method for motif discovery that overcomes limitations of existing approaches.
  • To improve the accuracy of identifying regulatory DNA motifs, particularly in divergent species.
  • To apply the method to discover cis-regulatory elements in yeast and insect genomes.

Main Methods:

  • A new algorithm integrating overrepresentation and evolutionary conservation properties of motifs.

Related Experiment Videos

  • Application to ChIP-chip data from Saccharomyces cerevisiae across four yeast species.
  • Analysis of cis-regulatory elements in ribosomal protein genes of two insect species.

    • Main Results:

    • The method achieved 20% higher accuracy in motif discovery compared to current state-of-the-art methods in yeast.
    • Successfully identified cis-regulatory elements controlling ribosomal protein gene regulation in distantly related insects.
    • Demonstrated robustness and applicability to genomes of divergent species.

    Conclusions:

    • The proposed method offers a significant advancement in motif discovery, especially for comparative genomics.
    • It enhances the extraction of regulatory signals from multiple, potentially divergent, genomes.
    • The findings have broad implications for understanding gene regulation across diverse taxa.