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Fig. 5 | Breast Cancer Research

Fig. 5

From: Separation of breast cancer and organ microenvironment transcriptomes in metastases

Fig. 5

Identification of genes within human metastasis signatures that originate from liver cells. a RNA-seq data from patient-matched breast tumors and liver metastases were downloaded from Siegel et al. [30], median centered, and hierarchically clustered. Highlighted in the purple box are 171 genes increased in each liver metastasis compared to the primary tumor it was derived from. b ANOVA was performed on the PDX mouse RNA-seq dataset for all 171 genes to identify the transcripts which were induced in the liver cell transcriptome during PDX metastasis compared to normal mouse liver. Twenty-four liver genes were identified as significantly upregulated (p < 0.05) in metastases compared to normal liver and were averaged to generate a signature value for each sample. PDX liver macro-metastases were used for the analyses that had human RNA content > 50% (n = 19), normal mouse liver (n = 3). c 27 liver relapses and 17 breast relapse fine-needle aspirates from Tobin et al. [31] were queried for the 27-gene liver microenvironment gene signature presented in Additional file 7c

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