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(a)–(c) show histograms of hypergeometric P-values. In panel (a), the P-values are computed for 1000 random gene sets with respect to the yeast interaction data set of Duan et al. (3). In panel (b) the P-values are computed with respect to a simulated data set for 250 random sets of 100 genes. In (c), the P-values correspond to 174 gene sets regulated by a single transcription factor and studied in (11), computed with respect to the yeast interaction data set of (3). Panels (d)–(f) are analogous to panels (a)–(c), but the P-values are computed using the resampling approach. In each case, the resampling-based P-values provide no evidence of colocalization of gene sets.