The loops between MSI and NRAS suggested two independent negative associations, one direct and the other indirect via CIN, TP53 and KRAS. Most intriguing was the loop between MSI and KRAS. Here, there existed not only a direct negative association between TP53 and KRAS mutations, but also a weaker, indirect positive association via CIN, MSI, KRAS and BRAF. The indirect positive association found by multivariate analysis was consistent with data in the literature from pairwise association testing, but the direct negative association was less well supported. This evidence concerns the gene KRAS and cervical squamous intraepithelial neoplasia.