Table 1

Correlation of Gene expression and SNP copy number
Gene expression Number of genes Number of SNPs with
Amplification Deletion No variation Total
up 330
104 3032 3494
down 170 121
1694 1856
479 145 4726 5350

The correlation between the top 500 differentially expressed genes and the copy number of SNPs found within the coding regions was examined. For each up- or down-regulated gene the number of SNPs with an increase (amplification), a decrease (deletion) or no variation in copy number were counted. All in all, 5,350 SNPs were found within differentially expressed 500 genes; 7.5% of them had significant variations in SNP copy numbers (underlined). For merely 358 SNPs within the 330 up-regulated genes, an increased copy number was detected. For the 170 down-regulated genes only 41 SNPs were found to have a decrease in copy number.

StandfuƟ et al.

StandfuƟ et al. BMC Cancer 2012 12:380   doi:10.1186/1471-2407-12-380

Open Data