PU.1-Directed Gene Networks in Erythroid Cells Figure 1. Genome-wide binding of PU.1 is very similar in ES-EP and MEL cells. (A) ChIP-Seq peaks were identified as described in Materials and Methods. A point represents the log2 of the number of sequence reads from ES-EP and MEL cells contained in a peak. Each peak was assigned to one of two categories based on the ratio of the number of reads in the two cell types. Peaks within a ratio #5 are classified as shared between both cell types (represented in light blue), whereas peaks with a ratio .5 are enriched in a cell specific manner (represented in red for ES-EP or dark blue for MEL cells). (B) Venn diagrams illustrate the number of peaks (left) or genes with a peak within 2 kb of TSSs (right) in ES-EP and MEL cells (colors as A). doi:10.1371/journal.pgen.1001392.g001 This analysis showed that genes differentially expressed $2-fold more in one cell type have higher PU.1 occupancy in that cell type (Figure 3A). This result suggests that, for genes differentially expressed between the two cell types, PU.1 occupancy often leads to upregulation of the gene’s expression in that cell type, and hence PU.1 is acting on such genes primarily as a transcriptional PLoS Genetics | www.plosgenetics.org 3 June 2011 | Volume 7 | Issue 6 | e1001392