PU.1-Directed Gene Networks in Erythroid Cells Figure 2. Properties of the PU.1 ChIP-Seq peaks in ES-EP and MEL cells. (A) Sample signal tracks of PU.1 ChIP-Seq data from MEL cells and ES-EP are shown for an ,500 kb region of chromosome 15 in the Integrated Genome Browser (IGB) (Affymetrix), with the y-axis representing the number of reads. Input DNA controls are also shown for both cell types. (B) Sequence logos for the enriched motifs within PU.1 ChIP-Seq peaks from MEL (left) and ES-EP (right) cells, derived from MEME motif analysis (see Materials and Methods). (C) The distance between each PU.1 ChIP-Seq peak and the TSS within 2 kb was computed and the results are binned and plotted for MEL (top left) and ES-EP (bottom left). Peaks were further annotated by their genomic locations with respect to current gene annotation (right) and classified as proximal promoter (+/22 kb of TSS), 39 end of gene (+/22 kb of TES), gene body (between +2 kb of TSS and 22 kb of TES), miRNA promoters, or otherwise intergenic regions. doi:10.1371/journal.pgen.1001392.g002 PLoS Genetics | www.plosgenetics.org 4 June 2011 | Volume 7 | Issue 6 | e1001392