Fig. 1

Changes in the global transcriptional profiles of MCF10A and MCF7 cells directly stimulated with recombinant TGFB1 (TGF) or exposed to conditioned media (CM). (a) Number of genes induced (log2FC > 1.0, padj < 0.05) or repressed (log2FC < − 1.0, padj < 0.05) after TGF or CM treatment. (b) Overlap of genes with altered expression after 6 days of TGF and/or CM treatment in both cell lines (see also Figure S3). (c) Heatmap with hierarchical clustering of normalized read counts from RNA-seq (row z-score) for selected genes (1,685) with altered expression after TGF treatment and their assignment to hallmark pathways (on the right). (d) Gene set enrichment analysis showing significant pathways from the hallmark gene set collection detected in MCF10A and MCF7 cells treated with TGF or CM, as well as differences between treatments and differences between cell types: untreated (Ctr, shown in green rectangle) and in response to TGF (first compared to corresponding Ctr). The sizes of the pie charts correspond to the effect size, while color intensity corresponds to the p value; blue and red indicate the fractions of downregulated and upregulated genes, respectively. The cells were treated according to the scheme shown in Figure S2a