Fig. 3

PcTF-expressing breast cancer cell lines show upregulation of interferon (IFN) pathway genes. a Charts show log10 (FPKM) of PcTF for untransfected cells (UT) and at 24, 48, and 72 h following transfection of each cell line. The outlier for BT-474 (48 h, replicate 1) was omitted from subsequent analyses. Dots, each replicate library; bars, mean of values from the two replicates. b Mean log10(FPKM) values are shown for 19 Polycomb-upregulated genes genes (PUGs; FC ≥ 2, q ≤ 0.05 at all time points in all three cell lines), sorted from lowest to highest average expression level in untreated cells. c Gene ontology (GO) Biological Process term enrichment for the 19 PUGs is represented the bubble chart. GO clusters and representative terms (black labels) are plotted based on semantic similarities in the underlying GOA database. d Overrepresentation of transcription factor (TF) binding motifs [74] at the promoters of PUGs (p-value < 0.05/19.0, Bonferroni correction). e Transcription factors (outermost boxes) associated with promoter motifs from panel D are shown in the network graph