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 HumanMethylation450 微珠甲基化芯片（Infinium HumanMethylation450 BeadChip）甲基化阵列数据开展分析，样本涵盖三阴性乳腺癌（Triple-Negative Breast Cancer, TNBC）、非三阴性乳腺癌（Non-TNBC）及正常组织三类。
(A) 针对每类样本（TNBC、Non-TNBC或正常组织）的β甲基化比率（甲基化信号/总信号）绘制原始核密度图（Kernel density plot）。
(B) 采用wateRmelon包[55]所实现的方法，对β甲基化比率进行分位数标准化（Quantile normalization）后绘制核密度图。
(C) 对经分位数标准化后的β比率进行对数变换（Logit transformation）得到M值（M-Values），并绘制其核密度图，展示峰值对齐情况。
针对TNBC与Non-TNBC的对比分析（D）以及TNBC与正常组织的对比分析（E）中的甲基化探针，绘制折叠变化（Fold Change, FC）与校正p值的火山图（Volcano plot）。其中，非差异甲基化探针（或虽为差异甲基化但校正p值>0.05的探针）以灰色圆点展示；高甲基化的差异甲基化探针以蓝色圆点展示，低甲基化者以红色圆点展示。折叠变化≥+2或≤−2且带有错误发现率（False Discovery Rate, FDR）的探针