PIK3CA and cervical squamous intraepithelial neoplasia: We found that the primary positive associations were between: (a) CIN and TP53; (b) MSI and BRAF; and (c) KRAS and PIK3CA. The primary negative associations were between MSI and both CIN and NRAS, and between KRAS and each of BRAF, NRAS and TP53. These associations are shown in a simple, graphical form in Figure 1A. In almost all of these cases, the network analysis found the same primary associations as the logistic regression analysis (Figure 1A; see also Supplementary material, Table S3).