Many of the ENCODE assays directly or indirectly provide information about the action of promoters. Focusing on the TSSs of protein-coding transcripts, we investigated the relationships among different ENCODE assays, in particular testing the hypothesis that RNA expression (“output”) can be effectively predicted from patterns of chromatin modifications or TF binding (“input”). Consistent with previous reports58, we observe two relatively distinct types of promoters: (1) broad, mainly C+G rich, TATA-less promoters; and (2) narrow, TATA-box-containing promoters. These promoters have distinct patterns of histone modifications, and TF-binding sites are selectively enriched in each class (Supplementary Figure Z1).
