Supplementary material: Linking Signaling Pathways to Transcriptional Programs in Breast Cancer


Figure S2. Performance of affinity regression using data from the TCPA RPPA data set



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Figure S2. Performance of affinity regression using data from the TCPA RPPA data set. (A) Cross-validation performance on held-out samples (indicated as circle data points) and performance on independent TCGA test set (indicated as triangle data points) show affinity regression outperforms nearest neighbor; (B) hierarchical clustering of inferred TF activities recovers major transcriptional subtypes.

Figure S3. Unsupervised hierarchical clustering of tumors of Basal-like, HER2, LumA and LumB subtypes by their sample-specific inferred transcription factor activity. As in Fig 2B, but showing all inferred TF activities. The bottom panel shows clinical features: coral (positive), blue (negative), white (NA).



Figure S4. Unsupervised hierarchical clustering of tumors of Basal-like, HER2, LumA and LumB subtypes by their sample-specific inferred protein activity. The clustering was performed using all features, but for readability only the features with largest standard deviations across samples are shown in the heatmap. The bottom panel shows clinical features: coral (positive), blue (negative), white (NA).





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