Using TCGA data, we selected patients with disease stage between I and III. After applying log transformation () we computed the quantiles of expression of MHC-II related genes. Patients were labeled as “low” if the expression of the gene in question was below the first quantile (25%) and “high” if it was higher than the third quantile (75%). Cell type enrichment analysis results for TCGA data were downloaded from the xCell website (https://xcell.ucsf.edu/) and patient groups were compared.
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