ArticleBMC bioinformatics2007
Statistical tests to compare motif count exceptionalities.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Statistical approaches to detecting and analyzing tandem repeats in genomic sequences.Frontiers in bioengineering and biotechnology · 2015Review
- Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila.Genes & development · 2014Article
- Repeat or not repeat?--Statistical validation of tandem repeat prediction in genomic sequences.Nucleic acids research · 2012Article
- A system of repressor gradients spatially organizes the boundaries of Bicoid-dependent target genes.Cell · 2012Article
- Identification and analysis of papillomavirus E2 protein binding sites in the human genome.Journal of virology · 2012Article
- DNA motifs that sculpt the bacterial chromosome.Nature reviews. Microbiology · 2011Review
- Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.PLoS computational biology · 2010Article
- Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast.BMC bioinformatics · 2008Article
- SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics.BMC bioinformatics · 2008Article
- Identification of DNA motifs implicated in maintenance of bacterial core genomes by predictive modeling.PLoS genetics · 2007Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundFinding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required.
resultsWe develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops.
conclusionThe exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.
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