Figure 3

Integrating cluster analysis and functional knowledge. Genes were clustered using the CSIMM [22] algorithm and variance-scaled data from two independent breast cancer datasets (GSE3494 [28] and GSE7390 [31]), and CLEAN scores were computed for both clusterings. The number of genes common in both datasets after filtering was 8,567. A) The gene-specific CLEAN scores for the two datasets were plotted against each other and the Pearson's correlation coefficient was computed. A small error was added in the scatter plot to better visualize overlapping data points. B) Pairwise similarity measures between genes computed by CSIMM were also plotted and correlated. C) Expression profiles of genes with the very highest CLEAN scores in both datasets showed strong co-expression in both datasets. All genes in this cluster are immunity related.