One-way complete linkage clustering of microarray data.

The custom microarray expression data of endothelial cells exposed to a variety of modulators was clustered on the basis of similar regulation patterns using GeneCluster/TreeView.20 HUVECs were exposed to a pulsatile shear stress of 19 ± 12 dyne/cm² in an artificial capillary system. Static cultures were stimulated with TNF-α, IL-1β, TGF-β, VEGF, or thrombin for 2, 6, and 24 hours. Expression profiles for HL-60, HeLa, and SMC cells were included after normalization to GAPDH. (A) The self-organizing map and hierarchical tree show the total cluster of all genes after data filtering, only including genes in the analysis that had hybridization signals above 10% of the GAPDH signal with at least one of the stimuli/conditions used. The 12 flow-responsive genes identified in this study are shown in blue. Specific clusters shown are genes induced exclusively by shear stress (B), genes induced by IL-1β and TNF-α (C), and genes induced by TNF-α and shear stress (D). Clusters shown in panels B-D are headed by a single row of colored squares representing the general trend of the cluster. Colors of the squares represent the relative expression of the genes in the condition given in the column heading as established after median centering of normalized hybridization signals. Red and green represent higher and lower expression than the median for that particular gene, respectively. Color intensity is related to the difference with the median (black).