EMT score
    To compute the EMT score of a sample, we obtained a list
    of 145 epithelial marker genes and a list of 170 mesench-
    ymal marker genes from a previous study [52], and then
    adopted a similar approach to that used in the prognostic
    signature of TCGA group [81]. The expression of the
    marker genes were first normalized across patients, and a
    Student’s t-test score comparing the expression of
    mesenchymal marker genes to epithelial marker genes was
    then taken as the EMT score. Therefore, a sample with
    EMT score > 0 reflects a more mesenchymal phenotype
    whereas an EMT score < 0 indicates a more epithelial
    phenotype.

    Recently, Rooney et al. described the cytolytic activity (CYT) score, which was obtained by calculating the geometric mean of granzymes A (GZMA) and perforin (PRF1) mRNA expression levels in tissue.