Fig. 4.

Unsupervised clustering of a 230 gene expression panel distinguishes HPV-positive from HPV-negative OPSCC. Total RNA from formalin-fixed paraffin embedded tumor specimens were run in duplicate using the NanoString Human Cancer Reference kit. One HPV-negative (HPV−_3) sample was removed from the clustering due to poor performance of housekeeping genes. Clustering clearly shows the reproducibility of technical replicates as well individual expression pattern of each tumor. Distinct subsets of differentially expressed genes are labeled C1-6 on the y-axis. A full list of these genes and normalized are available in the Supplemental Table (S1)