Parameters used and number of significant patterns discovered for each of the three datasets, for evaluating the effects of gene-set constraints on enhancing statistical power after correcting multiple hypothesis tests.

Parameters used and number of significant patterns discovered with respect to the FDR cutoff for each of the three approaches (A: without constraint, ; B: with constraints, and C: with constraints, ) on each of the four real datasets. The number outside the brackets are the number of significant patterns discovered, and the first number inside a bracket shows the number of unique SNPs covered by the patterns (note that there are overlaps between patterns); the second number inside the s bracket (for approaches B and C only) indicates the number of SNPs that are discovered by approaches B or C but not by approach A in the corresponding dataset, thus indicating the benefit of using gene-set constraints.