Fig. 2

Differential footprints reveal links between TF binding and gene expression. a Differential gene expression (p < 0.005, Mann–Whitney U test) of all genes that have a differential CD4 footprint containing a match for the T-box motif in their promoter. b Average bias-corrected DNase-seq cleavage profiles (red: positive strand cuts, green: negative strand cuts) centred on T-box motifs in promoters of genes from (a) show evidence for binding of T-box motifs in CD4+ cells, but not in spinal cord cells. Genes over-footprinted for T-box in CD4+ cells are also over-expressed, confirming a known lineage-determining link. c Differential gene expression of all genes that have a differential CD4+ DHS containing a match for the T-box motif in their promoter. d Average bias-corrected DNase-seq cleavage profiles centred on T-box motifs in promoters of genes from (c) do not show evidence for binding in either cell type. The differential expression observed in (c) cannot be linked to TF binding using differential DHS scores alone