Figure 6.

PU.1 extracts higher DNA site specificity than Ets-1 in vivo and in vitro. DNA site preferences in vitro by Ray-Gallet et al. (48) for PU.1 and Woods et al. (49) for Ets-1 were chosen among alternatives (21,46) for their larger sample sizes and sequence spaces. ChIP-Seq data for genomic preferences in vivo were as curated by the HOMER Motif Database for murine PU.1 (4) and human Ets-1 (50), the JASPAR Database for murine Ets-1 (MA0098), and the human ENCODE Consortium for human PU.1 (51). The data were analyzed for their information content (IC) and presented as DNA logos (47). The height of each stack represents the IC for that position, and summed to give the total IC for the 10-bp binding site. Although the total ICs differ depending on the experimental context, each matched pair of binding motifs differs by ∼2 bits.