Unsupervised gene differential coexpression analysis was used (73) to capture context-specific patterns of gene coexpression that revealed patient strata, i.e., groups of samples with coordinated expression. GimmR package with default options was used for differential coexpression analysis; clustering and heatmaps were generated using R package ComplexHeatmap. Strata identified in the CTSC discovery cohort by using the MG-154 metabolic signature, in conjunction with differential coexpression analysis, were subsequently characterized in terms of mutational profiles and association with smoking.

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