Genes associated with genotype-specific DNA methylation in squamous cell carcinoma as candidate drug targets

BMC Systems Biology

Table 6 t-tests of randomly sampled SNPs between genotype and DNA methylation.

Nsp
	Lower bound	Upper bound	Number of significant P- values
blood	6.9 × 10^{− 4}	1.00	19
normal tissue	0.32	1.00	0
tumor	0.96	1.00	0
Sty1
	Lower bound	Upper bound	Number of significant P- values
blood	0.05	1.00	5
normal tissue	0.01	1.00	4
tumor	0.04	1.00	6
Sty2
	Lower bound	Upper bound	Number of significant P- values
blood	6.12 × 10^{− 4}	1.00	2
normal tissue	0.06	1.00	0
tumor	9.56 × 10^{− 3}	1.00	1

P-values were computed using t-tests for the microarray measurements between genotype and DNA methylation for 1000 independent sets of randomly sampled SNPs. Each of the sets contained at least as many SNPs as are included in Table 4. Nsp and Sty are the microarray data sets used in the study. Sty1 and Sty2 correspond to the PC4 for genotype (Figures 4d and 6b)/ PC3 for DNA methylation (Figures 5c and 6c) and PC3 for genotype (Figures 4c and 6a)/ PC4 for DNA methylation (Figures 5d and 6d) combinations of PCs. P-values, adjusted by the BH criterion, of < 0.05 were regarded as significant.

ISSN: 1752-0509