Figure 4. Regulator co-occupancy matrices.
Shown are promoter co-occupancies and other related properties between 20,301 unique combinations of 202 regulator pairs. (A) Percent overlap for the set of genes co-occupied by each regulator pair is displayed as a heatmap. Each pixel represents the overlap in a Venn diagram between two regulators, heatmap color-coded in accord with the extent of overlap, as indicated. Overlaps that did not meet a significance threshold of P <10-5, or represented a self-by-self comparison were drawn as white pixels. Rows and columns were hierarchically clustered using Cluster (Eisen et al., 1998). See Figure S1 for high resolution images. A blow-up of a portion of cluster a (8 × 8 matrix) is shown in upper portion of the panel.
(B) Statistical significance (P-value determined by the Chi-test) of overlap for the set of genes co-occupied by each regulator pair is displayed as a heatmap. For panels B-D, pixels are in the same position as in A, and were colored white if they were white in panel A.
(C) The corresponding median transcription frequency for the set of genes co-occupied by each regulator pair is displayed as a heat map. Data for mRNA/hr is from (Holstege et al., 1998).
(D) If two compared regulators belonged to the same stage of the transcription cycle (Figure 1A), then the corresponding pixel was color-coded by the stage, as indicated. Otherwise they were colored white.