Figure 5

YMF scores for the REDfly analysis CRMs. (a) Histograms of percentage of CRMs for given P value ranges (YMF scores). The histogram for all 280 REDfly analysis CRMs is shown in blue ('CRMs'), for randomly selected non-coding sequences in green ('Random'), and for the random expectation ('Uniform') in red. (b) Cumulative histograms of YMF scores for tissue- and stage-specific CRM subsets. The entire REDfly analysis set is shown in blue and the expected uniform distribution in red. Solid green lines indicate the blastoderm CRMs, while dashed green lines represent the non-blastoderm CRMs; orange solid and dashed lines show the embryo and non-embryo CRM subsets, respectively. Note that all subsets show significant deviation from the expected uniform distribution. (c) Specificity/sensitivity curves for CRM prediction using YMF. Three sets of curves are shown, representing three different assumptions as to the number of CRMs present in the randomly selected background sequences: 25% CRMs (red), 50% CRMs (blue), and 75% CRMs (green). Solid lines indicate curves for the entire 280 REDfly analysis CRMs, while dashed lines show the blastoderm CRM subset. The black dashed line represents the curve for randomly selected sequences, shown for 50% background CRMs only. For each category, the random expectation is equal to the assumed number of CRMs in the background.