PPI numbers observed in gene pairs with different DNA-interaction levels. The x-axis shows the first, second, third and fourth quartiles of the DNA-interaction frequency (excluding non-contact) between gene pairs. “Non-contact” represents the gene pairs with no interaction information. The y-axis represents the observed PPI number per million DNA-interacting gene pairs. The corresponding P-values calculated using the Wilcoxon rank sum test are listed in Additional file 1: Table S3.