Table 1.

False positive rates at a nominal significance level of 0.05 in step 1

	CMC-1	CMC-count	WeightSum1	WeightSum2
Irrelevant genes	0.087	0.087	0.108	0.086
Irrelevant genes excluding spurious ones	0.060	0.060	0.059	0.052
Permutations	0.050	0.050	0.035	0.050

False positive rates were calculated by counting significant values in either irrelevant genes or in 2,000 permutation tests.