Analysis of relationships between mouse mammary tumor models. (A) Theunsupervised hierarchical clustering analysis of gene expression data for mousemammary tumors, cell types and normal mammary gland is shown. The dendrogramacross the top illustrates relationships between samples and is color-coded toitemize the four main clusters. Below the dendrogram, black bars label samplesfrom each corresponding model on the same line. Gene expression values areillustrated with the heatmap, according to the scale shown. The verticaldendrogram beside the heatmap illustrates genes with similar patterns ofexpression across the samples in the dataset. (B) The pie chartillustrates the gene ontologies of the genes that are significantly(q = 0, fdr = 0) over-expressed as identified by SAM inthe blue cluster of tumors compared to tumors in other clusters. (C) Thegene set enrichment plot comparing tumors from cluster 4 (black) to tumors inthe other clusters shows significant enrichment for high expression of a geneset that defines mesenchymal breast cancer (P = .004).SAM, significance analysis of microarrays.