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The enrichment of identified upregulated and downregulated gene set identified using the discovery set was assessed in TCGA cohorts using GSEA v2.2.2. GSEA computes the enrichment score by applying weighted Kolmogorov−Smirnov statistic to a running sum of the ranked list with 1000 permutations. The enrichment score (ES) was further normalized to account for the size of each inputted gene set. The false discovery rates (FDR) <0.001 were assumed to be statistically significant.
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