The dynamics of hormone-responsive gene expression is consistent with FFL network motifs. (A) BMMФ were treated with 100 nM Dex for indicated time and the expression levels of Dex-responsive genes were determined by RT-qPCR. (B) BMMФ were treated with Dex either alone or in the presence of the protein synthesis inhibitor Chx for 1–3 h; the expression of indicated genes were determined by RT-qPCR and expressed relative to transcript levels in the absence of Dex (‘Control’), with or without Chx (=1). (C) The dynamics of Klf2 expression is consistent with the I1-FFL with a strong repressor (R) as an intermediate regulator. Klf2 expression data (black circles) collected over 9 h was subjected to a global least square analysis (red line) using the equation (1) (Additional file 1). The quality of the fit as determined by calculating coefficient of determination R2 (Additional file 1) improved considerably when the expression data were limited to initial 4 h (green line). The numerical solution of the equation (3), which allows for variation in degradation rates of both “R” and Klf2, yields a better fit (blue line) to the Klf2 expression data. The R2 for curve fitting analyses are shown in the legend. (D) Glucocorticoid induction of Klf2 in BMMФ derived from Klf9-KO mice (red squares) loses peak-like kinetics, characteristic of I1-FFL controlled genes (blue diamonds). WT and Klf9-KO BMMФ were cultured in the presence of Dex for indicated time and the expression of Klf2, Tsc22d3 and Nr3c1 (GR) was assessed by RT-qPCR as in A. Basal levels of each transcript were set to 1 for untreated BMMФ of each genotype. Error bars are standard errors of the mean.