Table 1.

FDR for the tests on the absence of correlations between exons in human chromosomes and random sets

Number of points in random sets relative to that of exons	Fraction of events with P < 0.05 per 100 MC realizations
	Exons on forward strand			Exons on reverse strand
	2-Fold less	Equal, ±10%	2-Fold more	2-Fold less	Equal, ±10%	2-Fold more
Genomic HyperBrowser12,13
P-value, exon positions preserved, random set MC randomized	0.253	0.253	0.247	0.249	0.250	0.248
Adjusted P-value, exon positions preserved, random set MC randomized	0.227	0.228	0.227	0.227	0.231	0.228
P-value, random set preserved, exon positions MC randomized	0.538	0.597	0.670	0.588	0.635	0.773
Adjusted P-value, random set preserved, exon positions MC randomized	0.523	0.582	0.656	0.573	0.628	0.768
GenometriCorr14
Relative distance KS P-value, exons—reference; random—query	0.047	0.049	0.051	0.051	0.048	0.050
Absolute distance P-value, exons—reference; random—query	0.109	0.106	0.100	0.110	0.107	0.109
Relative distance KS P-value, random—reference; exons—query	0.537	0.437	0.428	0.579	0.450	0.215
Absolute distance P-value, random—reference; exons—query	0.705	0.697	0.662	0.725	0.693	0.599
Genome Track Analyzer
United z-criterion, Equation (23)	0.056	0.052	0.051	0.044	0.046	0.048

All tests were performed with predicted P-values <0.05. The expected mean value and standard deviation for FDR per 100 MC realizations should be 0.05 ± 0.005.

FDR, false discovery rate; MC, Monte Carlo; KS, Kolmogorov–Smirnov test.