High expression of oxidative phosphorylation genes predicts improved survival in squamous cell carcinomas of the head and neck and lung.

A parallel analysis performed for LUSC failed to detect any statistically significant differences between OXPHOG patients clusters 1 and 2 for any specific leukocyte subtypes; however, there was a trend for decreased cytotoxic cells in cluster 2 that became highly significant for remaining patient clusters (Supplementary Table 18 ) when compared to OXPHOG cluster 1.

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OXPHOG clustering reached statistical significance on univariate analysis of both datasets and approached significance on multivariate analysis in both datasets (Supplementary Tables 8 and 9 ).

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Transketolase like 2 (TKTL2) had a mutational frequency above 5% in LUSC, but failed to reach statistical significance by MutSiq analysis (Q-value= 0.06) 18 and demonstrated a random missense mutational pattern across the length of the gene (Supplementary Fig. 5 ), making it unclear whether the gene was a driver or passenger.

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We found a clear trend of increasing mitochondrial copy number with increasing expression of oxidative phosphorylation genes, although differences only reached statistical significance for OCSCC cluster 5 which had roughly three times less mitochondria than cluster 1, the lowest expression of oxidative phosphorylation genes, and poor survival.

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