(A) Mouse embryonic palatal mesenchyme (MEPM) cells were dissected from E13.5 embryos, passaged twice, and then serum starved overnight prior to stimulation with either PDGFAA or FGF1 + heparin. (B) Expression of all genes with FPKM (fragments per kilobase of exon per million reads mapped) >1 at 1 hr (11,217 genes) and (B') 4 hr (11,266 genes). Genes colored blue are significantly increased with fibroblast growth factor (FGF) treatment and genes colored red are significantly increased with platelet-derived growth factor (PDGF) treatment. Values plotted on log2 scale. (C) Fold change (FC) comparison for all differentially expressed (DE) genes at (C) 1 hr or (C') 4 hr (compared to serum starved sample) shows high correlation between the transcriptional response to each growth factor at 1 hr but low correlation at 4 hr. (D) Protein–protein interaction (PPI) network for all genes upregulated at 1 hr contains many classic immediate early genes (such as AP-1 components, Myc, and Srf). Genes are colored based on their primary reported role in transcriptional regulation (22, 23), with orange squares representing activators and gray circles representing repressors. (E) FC (compared to untreated sample) for selected genes upregulated at 1 hr. Genes in bold are induced >1.5-fold in response to the indicated growth factor. Although both PDGF and FGF regulate many shared targets, the induction in response to FGF exhibits greater magnitude (Fos, Fosb, Junb, Atf3, Egr1, Egr2) and longer duration (Fos, Fosb, Jun, Junb, Egr1, Egr2).