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Related Experiment Videos

Statistical tests to compare motif count exceptionalities.

Stéphane Robin1, Sophie Schbath, Vincent Vandewalle

  • 1INA PG/ENGREF/INRA, UMR518 Unité Mathématiques et Informatique Appliquées, 75005 Paris, France. robin@inapg.inra.fr

BMC Bioinformatics
|March 10, 2007
PubMed
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Comparing motif exceptionality across two biological sequences requires statistical tests beyond simple p-value comparisons. This study introduces two new tests to determine if a motif

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying over- or under-represented motifs in genomic sequences is crucial for functional analysis.
  • P-values for motif counts identify exceptional motifs but do not allow direct comparison of exceptionality between two sequences.
  • A statistical test is needed to rigorously compare motif exceptionality across different biological sequences.

Purpose of the Study:

  • To develop and analyze statistical tests for comparing the exceptionality of a specific motif in two distinct biological sequences.
  • To provide a method for determining if a motif's significance differs significantly between two sequence sets.

Main Methods:

  • Development of two statistical tests: an exact binomial test and an asymptotic likelihood ratio test.

Related Experiment Videos

  • Modeling motif occurrences using Poisson processes, accounting for overlapping motifs.
  • Incorporation of sequence composition into the statistical models.

    • Main Results:

    • The proposed tests effectively compare motif exceptionality between two sequences.
    • The tests can account for sequence composition and overlapping motifs.
    • An illustrative example compares octamer exceptionality in *Escherichia coli* K-12 backbone versus strain-specific loops.

    Conclusions:

    • The exact binomial test is suitable for small motif counts.
    • The likelihood ratio test is recommended for large counts due to its simplicity and correlation with the exact test.
    • Both tests provide a statistically sound method for comparing motif exceptionality.