RRHO Maps are a sensitive method for detection and visualization of overlap in expression data. Three representations of overlapping published cancer-related gene-expression signatures: signatures with strong (**A–C)**, medium (**D–F**) and weak (**G–I**) overlap represented as metric scatter plots (A, D and G), rank–rank scatter plots (B, E and H) and hypergeometric overlap maps (C, F and I). The first row of metric scatter plots show genes plotted by their direction-signed (up, positive; down, negative), log_{10}-transformed *t*-test *P*-values in each experiment; genes significantly changing in the same direction in both experiments are in Cartesian quadrants I and III and in opposite directions in quadrants II and IV. The Spearman’s ρ and Kendall’s τ rank correlation coefficients are indicated. The second row of rank–rank scatter plots show each gene plotted by its rank based on this metric. This representation spreads the genes more evenly across the plot and allows for assessment of overlap by increases in local density. The resulting plots show a higher density of genes along the diagonal in both the strong and medium overlap cases, especially at the bottom left and top right regions. The last row shows the rank–rank hypergeometric heatmap for each of these comparisons, where the overlap is represented statistically based on the hypergeometric distribution allowing visualization of any signal, even those that are relatively weak but significant. The log_{10}-transformed hypergeometric *P*-values are indicated in the color scale bar with negative values indicating under-enrichment. Sample permutation *P*-values based on the sum of the signal in the bottom left and top right regions are indicated (perm pval).

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