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. Author manuscript; available in PMC: 2019 Jun 15.
Published in final edited form as: Cancer Res. 2018 Apr 26;78(12):3375–3385. doi: 10.1158/0008-5472.CAN-17-3464

Figure 3.

Figure 3

Associations between DNA copy number and gene expression in head and neck squamous cell carcinoma by human papillomavirus (HPV) infection status. (A) Genome-wide plot of smoothed gene-level Pearson correlation coefficients between quantitative measurements of DNA copy number and gene expression for samples with (HPV+, n = 36) and without (HPV−, n = 243) HPV. Pronounced differences are observed at select genes. (B, D, F, H) Heatmap displays of gene-level quantitative DNA copy number measurements in select chromosomes. Genes are ordered by genomic position (columns); samples appear in rows and are hierarchically clustered according to HPV status. Rectangles highlight select regions containing driver genes with recurrent copy number changes. (C, E, G, I) Scatterplots of quantitative measurements of DNA copy number and gene expression for select genes of interest by HPV status.