Statistical analysis
Statistical analysis of gene expression data was applied to
log2-transformed values 22. A gene was
considered differentially expressed between tumors and controls if the
p-value was lower than 0.05 (FDR-corrected ANOVA). Sample clustering was
performed using the k-means algorithm with 1000 random permutations and
four different centroids. Centroid numbers were estimated using the
elbow method and UPGMA hierarchical clustering; input data were scaled,
centered and PCA transformed prior to clustering procedure.
Differentially expressed genes were identified by analysis of variance
(ANOVA) 23 between sample sets 1, 2 and 3. All
analyses were performed using R (version 3.4.4), with the following
packages: STRINGR, GGPLOT2, GRID, gridExtra, and GGBIPLOT.