Supplementary Figure 2. Sensitivity Analyses
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Significance After Multivariate: TNBC
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Signatures
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Supplemental Figure S2. Sensitivity Analyses For the Median-Center and Proliferation Normalization of Microarray Data.
A/B/C. Parallel coordinates plot of FDR p-value of all 125 signatures in ‘Original’ analysis versus multivariate analysis with study and/or estrogren
receptor (ER) as covariates for ER+/HER2- (A.), triple-negative breast cancers (TNBC; B.), or basal-like breast cancer (C.). D. Unsupervised hierarchical
cluster heatmap of all 125 signatures (y-axis) in 1033 patients in original Affymetrix dataset (top panel); after normalization using 11-gene PAM50
proliferation index (middle panel); and after normalization using the 131-gene PCNA proliferation signature (lower panel). Cluster of proliferation
signatures indicated in red box. E/F/G. Venn diagrams of the number of signatures (E.) or individual genes (F/G.) significantly associated with response
in original dataset (red) versus proliferation-normalized dataset (purple) using the 131-gene PCNA proliferation signature (E/F.) or 11-gene PAM50
proliferation index (G.). TNBC, triple-negative breast cancer; ESR1+/ERBB2- indicates tumors positive for ESR1 gene expression and negative for
ERBB2 gene expression.
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