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Related Experiment Videos

Assessing clusters and motifs from gene expression data.

L M Jakt1, L Cao, K S Cheah

  • 1Department of Biochemistry, University of Hong Kong, Pok Fu Lam, Hong Kong.

Genome Research
|January 13, 2001
PubMed
Summary
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We developed a novel method to assess gene clusters and regulatory motifs, identifying a link between Swi Five Factor and yeast forkhead proteins. This approach enhances the analysis of large-scale gene expression data for predicting cellular regulatory processes.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Large-scale gene expression and genomic sequencing generate vast data for identifying cellular regulatory processes.
  • Gene clustering based on expression profiles or function can group genes regulated by common transcription factors.
  • Identifying cis-regulatory elements in noncoding regions of clustered genes is crucial but challenging.

Purpose of the Study:

  • To develop and validate a computational method for assessing the functional significance of gene clusters and regulatory motifs.
  • To overcome difficulties in gene clustering and determining the relevance of sequence motif matches.
  • To identify potential functional relationships between transcription factors and gene sets.

Main Methods:

  • Developed a probability-based method to assess motif significance within gene clusters.

Related Experiment Videos

  • Utilized hypergeometric distribution to calculate the probability of motif matches by chance.
  • Employed multiple sample sizes of top motif matches to avoid threshold issues and detect weak/strong motifs.
  • Applied the method to yeast gene clusters and various motifs.

    • Main Results:

    • The method successfully assessed the significance of gene clusters and motifs.
    • Detected significant matches to motifs across cluster boundaries.
    • Identified a similarity between Swi Five Factor and forkhead proteins in yeast.
    • Provided evidence suggesting Swi Five Factor is a yeast forkhead protein.

    Conclusions:

    • The developed method provides a robust assessment of gene cluster and motif functional significance.
    • This approach aids in the discovery of transcription factor-gene relationships.
    • The findings suggest a novel classification for the Swi Five Factor, linking it to the forkhead family in yeast.