Figure 1.

Gene expression patterns of lymphoma cell line OCI-Ly3 treated with flavopiridol. (a) Hierarchical clustering of OCI-Ly3 cells treated with 60 nM, 300 nM, or 1 μM flavopiridol for 1 or 3 h. Each column is a single experiment comparing two cDNA populations; treated sample was labeled red (Cy5) and untreated sample was labeled green (Cy3). Each row represents data from a single cDNA microarray spot. The red-to-green (Cy5/Cy3) ratio reflects hybridization to that spot, a measure of relative gene expression; intensity reflects the magnitude of the difference between the samples according to the ratio color scale. Red indicates Cy5/Cy3 ratios >1, green indicates Cy5/Cy3 ratios < 1, black indicates no significant change in gene expression, and gray indicates the spot did not meet data selection criteria. These ratios were depicted according to the color scale shown at the bottom. (b) MTT assays. OCI-Ly3 cells were treated with increasing concentration of flavopiridol (0 to 2 μM) for 8, 24 or 48 h. MTT was added to the cells 2 h before harvesting. The plate was read at 570 nm. The result was shown as percentage of control versus flavopiridol concentration. (c) Hierarchical clustering of OCI-Ly3 cells treated with flavopiridol (1 μM), roscovitine (25 μM), or 9-nitropaullone (2.5 μM) for 1 or 4 h. These concentrations were chosen to give roughly equivalent (approximately 50%) cytotoxicity at 24 h without significant loss of cell viability at 8 h. The treated samples were labeled red (Cy5) and untreated samples were labeled green (Cy3). Only genes that were downregulated by more than threefold in one or more samples were extracted for clustering.