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

本研究对来自876份癌症基因组图谱（The Cancer Genome Atlas, TCGA）样本的Infinium人类甲基化450微珠阵列（Infinium HumanMethylation450 BeadChip）甲基化数据展开分析，样本涵盖三阴性乳腺癌（Triple-Negative Breast Cancer, TNBC）、非三阴性乳腺癌（Non-TNBC）与正常组织。(A) 各类别（三阴性乳腺癌、非三阴性乳腺癌或正常组织）的β甲基化比值（甲基化信号/总信号）原始核密度图。(B) 经wateRmelon包[55]实现分位数标准化后的β甲基化比值核密度图。(C) 经分位数标准化的M值（β标准化比值的logit变换）核密度图，展示了峰位对齐情况。针对三阴性乳腺癌与非三阴性乳腺癌（D）、三阴性乳腺癌与正常组织（E）的比较，绘制了甲基化探针的倍数变化（Fold Change, FC）与校正后p值火山图。非差异甲基化（DM）探针（或校正后p值>0.05的差异甲基化探针）以灰色圆点呈现；高甲基化的DM探针以蓝色圆点展示，低甲基化的DM探针以红色圆点展示。对于倍数变化≥+2或≤−2且错误发现率（False Discovery Rate, FDR）