Flowchart of the main steps in this study. Step 1 is the identification of genomic regions marked by one or more histone modifications or transcription initiation events. In step 2 genomic regions are clustered according to their features and enhancer regions are defined. In step 3, enhancers are further classified into 13 classes according to the pre-stimulation binding by six principal TFs. We perform various more detailed analyses on these 13 classes of enhancers in step 4, including analysis of gene expression of nearby genes, binding by additional TFs, and changes in binding by principal TFs after stimulation. Main input data are marked in grey.