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Fig. 2 | Clinical Epigenetics

Fig. 2

From: MethCORR infers gene expression from DNA methylation and allows molecular analysis of ten common cancer types using fresh-frozen and formalin-fixed paraffin-embedded tumor samples

Fig. 2

Molecular subtyping with MethCORR inferred RNA expression. a Scatterplot with the first- (PC1; X-axis) and second principal component (PC2; Y-axis) from a PCA performed with iRNA expression calculated for 738 TCGA BRCA samples with available estrogen receptor (ER) status. b Caleydo StratomeX [40] plot showing the concordance between PAM50 breast cancer subtype predictions made with RNA or iRNA expression as input for the TCGA BRCA cohort. Only samples with a confident subtype call for both input types are shown (n = 581; confidence = 1). c Kaplan–Meier plots showing the overall survival of AJCC stage I-IV patients from the TCGA BRCA cohort stratified according to PAM50 subtypes using either RNA-based (left panel) or iRNA-based (right panel) PAM50 subtype calls (for all confidence levels). Significance was evaluated by the log-rank test. In parenthesis is provided the Bonferroni-adjusted P values (two comparisons, i.e., LumA vs. HER2 and LumA vs. Basal). d Scatterplot with the first- (PC1; X-axis) and second principal component (PC2; Y-axis) from a PCA performed with TCGA BRCA RNA expression, TCGA BRCA iRNA expression, and iRNA expression calculated in an independent breast cancer FFPE cohort (GSE117439) for the PAM50 genes. Samples are colored according to their predicted subtype. Only samples with a confident subtype call are shown (confidence = 1). e Caleydo StratomeX plot showing the concordance between prostate cancer subtype predictions (ConsensusClusterPlus) made with RNA or iRNA expression as input for 497 TCGA PRAD tumor samples. f Caleydo StratomeX plot showing the concordance between lung cancer subtype predictions made with RNA or iRNA expression as input for 454 TCGA LUAD tumor samples. PI: Proximal Inflammatory, PP: Proximal Proliferative, TRU: Terminal Respiratory Unit. g Scatterplot with the first- (PC1; X-axis) and second principal component (PC2; Y-axis) from a PCA performed with TCGA LUAD RNA expression, TCGA LUAD iRNA expression, and iRNA expression calculated in an independent fresh-frozen cohort (GSE86836) for the 474 centroid genes used for subtyping. Samples are colored according to their predicted subtype

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