PU.1-Directed Gene Networks in Erythroid Cells Figure 5. PU.1 regulates many genes in the PI3K/Akt and ERK/MAPK signaling pathways. (A) and (B) IPA analysis was performed as described in Materials and Methods on PU.1 target genes in both ES-EP and MEL cells. The PI3K/Akt and ERK/MAPK signaling pathways were identified as being significantly over-represented among those genes. The left part of each panel depicts all of the components of the indicated IPA pathway. Components denoted with a filled yellow circle indicate that the gene for that component is associated with a PU.1 ChIP-Seq peak in both ES-EP and MEL cells. To the right of each pathway is shown the results of gene expression analysis of the indicated genes in early erythroid progenitors derived from wild-type embryos relative to PU.1 low embryos. doi:10.1371/journal.pgen.1001392.g005 specific transcription factors to modulate gene expression [17,29]. To identify candidate transcription factors that may cooperate with PU.1 in immature erythroid cells, we scanned the DNA sequences within the shared PU.1 peaks in ES-EP and MEL cells for potential transcription factor binding sites using the TRANS- FAC database (see Materials and Methods). The analysis revealed PLoS Genetics | www.plosgenetics.org 8 June 2011 | Volume 7 | Issue 6 | e1001392