Hierarchical cluster analysis of gene expression estimates from the expresssion microarrays and the heat map of binding ratios of the ChIP-chip experiments of the 150 TGF-β/SMAD target genes in IOSE cells. Genes that showed both altered expression at 3, 6, or 12 hrs relative to 0 hr (low-green and high-red) and altered binding at 3 hrs compared to 0 hr (low-white and high-blue) after TGF-β signaling stimulation were shown. The expression data were median-centered and normalized to have a unit sum of squares for each gene before transforming to the color scale. Genes that were confirmed by ChIP-PCR and RT-PCR are indicated by asterisks. Results from the ANOVA analysis indicating the peak time point relative to 0 hr is indicated by a color bar. The experiments labeled R1 were biological replicates in the expression microarrays and were technical replicates in the ChIP-chip experiments. In the Chip-chip experiments, normalized binding ratios to have a unit sum of squares for each gene were used for the heatmap.
Qin et al. BMC Systems Biology 2009 3:73 doi:10.1186/1752-0509-3-73