Global gene expression profiles in response to disturbed flow in mouse carotid artery endothelium in vivo. Total RNAs were obtained from intima of mouse left carotid (flow-disturbed, LCA) and right carotid (contralateral control, RCA) 12 and 48 hours after ligation. Illumina BeadChips containing 45 281 mouse genome-wide probes were used for the array study. Scatter plots show normalized intensities of each probe under 2 experimental conditions: LCA versus RCA at 12 hours (A) and 48 hours (B) after ligation. Genes that were up-regulated (red) or down-regulated (blue) (≥ 1.5-fold) at the FDR (≤ 10%) in LCA compared with RCA. (C-D) Hierarchical clustering analyses of mechanosensitive genes found in LCA endothelium compared with that of RCA are shown as heat maps. Each column represents a single sample pooled from 3 different LCAs or RCAs, and each row represents a single gene probe. (E) Venn diagrams show the temporal effects of disturbed flow on the number of up- or down-regulated mechanosensitive genes.