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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Analysis tools for the interplay between genome layout and regulation

Fig. 2

“Periodobar” of the detected periods for CRP target genes. Height of the bars indicates the significance of each period (-log(p-value) means that higher bars will depict lower normalised p-values -see text). The length of each period (in bp) is represented on the horizontal axis (logarithmic scale). The horizontal dashed line indicates the user specified p-value significance threshold and the vertical dotted lines signify the periods which are more significant than this threshold. A dashed line connects the tip of all the period bars to provide an overview of regions with dense periodic signal. The plot provides a quick and informative overview of periodicities in the genomic feature of interest (here the E. coli CRP regulon). CRP target genes exhibit four significant periods (exact length printed in the plot) and with the 2nd and the 4th being double the size of the 1st and the 3rd respectively. This particular finding corresponds to the existence of families of periods which are “harmonic” and constitutes an additional evidence for the validity of the periodicity of the CRP targets along the genome. (The plot was generated with 289 CRP target genes (98 data points left after the proximity removal) and p-value selection cut-off 0.05)

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