Fig. 3.

Virtual dissection of PDX mammary tumors and metastases into cancer (human) and microenvironment (mouse) gene expression datasets. The 134 sample RNA-sequencing dataset; PDX mammary tumors and metastases to the brain, lung, and liver; normal mouse brain, lung, and liver; 100% human breast tumors and brain metastases. a The transcripts from the 134 samples were segregated into human and mouse datasets; shown is the percent of each genome within each sample. b One mammary tumor from each PDX line was used in a Principal Component Analysis based on the 2000 most variable genes. c Mouse transcripts from metastases to the brain, lung, and liver, as well as normal mouse brain, lung, liver, were used to cluster the mouse genome based on the most variable top 2000 genes. d PDX tumors and metastases with more than ten million human mapped transcripts were combined with RNA-seq data from 817 tumors from The Cancer Genome Atlas. The PAM50 genes were used to hierarchical cluster the combined dataset