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. 2016 May 4;2:16007. doi: 10.1038/npjbcancer.2016.7

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Copyright © 2016 Breast Cancer Research Foundation/Macmillan Publishers Limited

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Expression characteristics of cancer-adjacent tissue samples. (a) Unsupervised gene expression clustering of RNA-sequencing data reveals two main clusters. Colored bars represent PAM50 subtype and miRNA subtype based on consensus cluster, and active/inactive subtype from Roman-Perez et al.¹³ (b) Normalized abundance heatmap for the a two-cluster NMF consensus clustering solution for microRNA profiles for 102 cancer-adjacent normals, for the 90 mature strands that had an absolute value fold change of at least 1.5 and a mean RPM of at least 25 in at least one of the two clusters. Below the heatmap, the silhouette width profile (W _cmm) calculated from the consensus membership matrix. The covariate track shows samples scored as active versus inactive from mRNA data. (c) miRs that were differentially abundant (FDR<0.05) between two unsupervised clusters, for the largest 25 fold changes (FC), for miRs with FC>1.5 and a mean (RPM)>25 in at least one of the two clusters. (d) Association of mRNA clusters with fat, stromal, and epithelial percentages in normal tissues. FDR, false discovery rate; NMF, non-negative matrix factorization.