A gene ontology (GO) analysis of Bptf-dependent expression datasets revealed an over representation of genes with “transcription factor activity”, genes involved in the biological processes of “development” and “morphogenesis” and the cellular processes of “cell death” and “cell proliferation” (Figure S18). Notable gene clusters include the consistent activation of genes correlated with “nervous system development” in all datasets, the repression of MHC I and II receptors during LIF−differentiation, the activation of genes correlated with “cytoskeletal components” during RA differentiation (Figure S18). In addition, we observed a striking over-representation of homeobox transcription factors within the “transcription factor activity” annotation. The homeobox-containing genes were almost exclusively up-regulated in each of the expression categories, and in some cases include almost the entire Hox gene cluster, indicating that Bptf is required for their repression in ES cells (Figure S19A, Figure S19B).
