Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis
Figure 6
The Association of Epithelial–Mesenchymal Transition with Histological Grade
(A) For each major breast cancer cohort where grade information was available, we give the heatmap of component expression values for the component enriched for the EMT pathway characterised in [41]. Thus, the heatmap matrix shown is SgkAks where k is the component enriched for the EMT pathway, g is any gene found on the array that is also in the pathway and the selected feature set of the component, and s denotes the tumour sample. The ICA algorithm for which this heatmap is shown is the KernelICA algorithm. Samples have been ordered according to a k-means (k = 2) clustering over the set of genes. Blue denotes “upregulation,” yellow “downregulation.” For the samples, histological grade is colour-coded as black (high-grade), blue (intermediate grade), and skyblue (low-grade).
(B) For each major breast cancer cohort, we give the heatmap of expression values for the same set of genes as in (A). Thus, the heatmap matrix shown is Xgs where Xgs denotes the measured expression level of gene g in sample s. As before, samples have been ordered according to a hierarchical clustering over the represented genes. Red denotes relative overexpression, green underexpression. Magenta denotes the upregulated cluster, cyan the downregulated cluster.