A List of Figures

Main Figures

Figure 1: NMU-induced mammary tumors

• Fig 1F: Characterisation HR plot
• Fig 1G: Ep DEG big-small
• Fig 1H: Ep hairball with size
• Fig 1I: summary of mutation burden
• Fig 1J: Frequency of different mutational codons
• Fig 1K: summary of mutations acccording to frequency cosmic
• Fig 1L: summary of metacore common mutated pathways

Figure 2: Immune system of NMU-rat

• Fig 2D: Differential CD45 genes
• Fig 2E: CD45 growing vs stable hairball
• Fig 2F: CIBERSORT shit
• Fig 2H: bcr clonotypes in tumor and normal mammary glands

Figure 3: Immunotherapy applied to NMU rats

• Fig 3B: Growth rates of tumors
• Fig 3C: Growth rates of tumors w.r.t. treatment
• Fig 3D: Histogram of growth rates of tumors
• Fig 3E: Contingency table growth rate and treatment
• Fig 3G: Trichrome staining growth rate and treatment
• Fig 3J: Differentially expressed genes in CD45 fraction

Figure 4: Characterizing CD45 cells in tumors

• Fig 4B: association of frequency with treatment and growth
• Fig 4C: KNN distances
• Fig 4D: interacting fraction
• Fig 4E: MH index with CD8 growth
• Fig 4F: Progression CIBERSORT TIMER
• Fig 4G: volcano plot of DEG stable vs growing CD45
• Fig 4H: CD45 cells enriched pathways
• Fig 4I: BCR clonotypes with respect to treatment/growth

Figure 5 : Epithelial cells in growing vs stable rats

• Fig 5A: GSEA summary stable growing
• Fig 5B: ssGSEA scores for specific pathways
• Fig 5D: CD74 assoc with patient data
• Fig 5E: forest plot CD74
• Fig 5F: lum only non-inflamm growth vs stable DEG
• Fig 5G: lum only non-inflamm growth vs stable hairball
• Fig 5H luminal signature associated with clinical variables
• Fig 5I OS and DFS for growing signature
• Fig 5J TCGA DEG for LumA samples
• Fig 5K TCGA HAIRBALL for LumA samples