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Table 4 Significance of the impact of individual parameters on the accuracy of discovered motifs

From: Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

Parameter Better Worse N Sup Inf Equal P-value
Background model taxfreq monad 20 20 0 0 9.54E-07
Dyad filtering filtered not filtered 20 20 0 0 4.78E-05
Taxon Gammaproteobacteria Bacteria 8 8 0 0 0.004
Taxon Proteobacteria Bacteria 8 8 0 0 0.004
Taxon Enterobacteriales Escherichia 8 6 2 0 0.020
Taxon Gammaproteobacteria Escherichia 8 6 2 0 0.020
Taxon Gammaproteobacteria Proteobacteria 8 6 2 0 0.034
Taxon Proteobacteria Escherichia 8 6 2 0 0.070
Taxon Enterobacteriales Bacteria 8 6 2 0 0.074
Promoter orthologs operon leader 20 13 5 2 0.107
Taxon Bacteria Escherichia 8 4 4 0 0.191
Taxon Gammaproteobacteria Enterobacteriales 8 5 3 0 0.273
Taxon Enterobacteriales Proteobacteria 8 4 4 0 0.528
  1. Parameters are sorted according to the significance of their impact on the geometric accuracy. The best parameter value of each pair is in the left column. N: number of parametric combinations. Sup, inf, equal: number of pairs where the left value gives better, wose or identical results than the right value, respectively. The P-value is estimated with a Wilcoxon paired test.