Additional file 15: Figure S8. of Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer

Analysis of Infinium HumanMethylation450 BeadChip methylation array from 876 TCGA samples, including TNBC, Non-TNBC and normal tissues. (A) Raw Kernel density plot from β methylation ratios (methylated / total signal) for each category (TNBC, Non-TNBC or normal tissue). (B) Quantile normalized Kernel density plot of β methylation ratios, as implemented by wateRmelon [55]. (C) Quantile normalized Kernel density plot of M-Values (Logit transformation of β normalized ratios), showing the peaks alignment. Volcano plot of the FC and adjusted p-values of the methylation probes in TNBC vs Non-TNBC (D) and TNBC vs normal (E) comparisons. Non-differentially methylated (DM) probes (or differentially methylated one but with p-value >0.05) are shown as gray circles. DM probes are shown as blue circles when hypermethylated and red circles when hypomethylated. Probes with a FC ≥ +2 or an FC ≤ −2, with an FDR < 0.05, were considered hyper- and hypomethylated, respectively. The numbers outside of circles refer to all probes that passed the FDR cutoff, while the numbers inside of circles are DM probes that passed both the FDR and fold-change cutoffs (XLSX 45499 kb)