NOJAH genome-wide heatmap (GWH) analysis of RNA-Seq derived gene expression data using TCGA BRCA expression dataset.

A) Genome-wide dendogram based on 50,248 genes using row normalization, 1-pearson correlation distance and ward.D clustering showing two clusters; one cluster containing many early survival time patients and the other, a mixture of early and late. B) Defining Core Genes. Distributions of measures of spread, VAR (variance), MAD (median absolute deviation), and IQR (inter-quartile range) shows IQR with fewer gene outliers as compared to VAR and a greater spread as compared to MAD. An ordered plot of IQR values for each gene shows 99th percentile as a cut point to define 605 topmost variable genes (a.k.a., ‘core gene set’). C) Heatmap of Core Genes. Heatmap using core gene set with options: z-score based row and column normalization, 1-pearson correlation distance, and agglomerative ward.D linkage shows two distinct gene and sample clusters. D) Defining Number of Clusters. Results from consensus clustering using 1-Pearson correlation distance, average clustering, 80% item resampling, 100% gene samples, and agglomerative hierarchical clustering shows two clusters in the data. E) Defining Core Samples. Silhouette plots of samples within each of two clusters. Samples with a silhouette-width less than 0.15 and 0.34 in clusters 1 and 2 respectively were removed to define the ‘Core subset’ of 12 and 5 samples respectively. F) Heatmap of Core Genes with Core Samples. Updated heatmap with options: row and column z-score normalization, 1- Pearson correlation distance, and agglomerative ward.D linkage clustering, based on core genes with core samples shows two distinct gene and sample cluster with most early survival time patients in one cluster and those with late times in the other.