Figure 4: Correlations of pseudogene expression subtypes with other tumour subtypes. | Nature Communications

Figure 4: Correlations of pseudogene expression subtypes with other tumour subtypes.

From: The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes

Figure 4

(a) Concordance between pseudogene expression subtypes and molecular subtypes defined by other genomic data in seven TCGA cancer types. Pseudogene expression subtypes were defined based on the expression of 500 pseudogenes with the most variable patterns through unsupervised analysis using NMF29. The colours indicate the statistical significance of the χ2 tests for assessing the concordance between the pseudogene expression subtypes and other molecular subtypes. (b) Concordance between pseudogene expression subtypes and other subtypes in BRCA. Pseudogene expression: subtype 1, red (n=144); subtype 2, green (n=390); subtype 3, and purple (n=303). PAM50 subtypes: basal-like (brown), HER2-enriched (dark green), luminal A (blue), luminal B (aquamarine) and normal-like (yellow). The status of ER, PR, HER2 or N is marked in black (positive) and white (negative); T status is marked in black (T2–T4) and white (T1). Mutations of TP53, PIK3CA, GATA3, MAP3K1 and MAP2K4 are marked in red. Correlations were assessed by χ2 tests.

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