Fig. 3

Klf9 associates near transcription sites and is more likely to be associated with repressed than induced genes. a Distribution of Klf9 peaks with respect to transcription start sites (TSS). b Distribution of Klf9 peaks with respect to gene features. c Overlap of Klf9-regulated genes with genes containing Klf9 peaks within 10 kb of their TSS. d The median expression ratio of all genes expressed in HT22 cells, with or without associated Klf9 peaks, in parent HT22 and HT22 [TR/TO-Klf9] cells treated with vehicle or doxycycline (1 μg/ml) for 8 h. In the parent cell line there was no expression difference after dox treatment whether or not the genes have Klf9 peaks associated (within 10 kb of their TSS; p = .057; Mann–Whitney U-test). In the HT22 [TR/TO-Klf9] cell line treatment with dox caused a statistically significant decrease in median expression ratio, but only for genes with associated Klf9 peaks (p < .001; Mann–Whitney U-test)