Cluster analysis of genes subject to regulation by Epo/SCF-controlled mRNA polysome recruitment and their regulation during differentiation. (A,B) Cells from the I/11 and R10 line were factor-deprived for 4 hours and stimulated with Epo plus SCF (ES) or left untreated (NF) for 2 hours. Total RNA and polysome-bound (pb) mRNA were isolated and used for RNA profiling on MG_U74Av2 Affymetrix oligonucleotide arrays. For each of 2 biologically independent experiments (I/11a and I/11b; R10a and R10b), the ES/NF ratio of intensity data was calculated. Significant variance between ES/NF ratios obtained with total and pb RNA was calculated using ANOVA (P = .01). In addition, differential expression in at least 2 single experiments had to be significant (P = .001). This selection yielded 115 probe sets. For these genes, the expression ratios after 48- or 60-hour differentiation induction were calculated compared with proliferation conditions (diff t48/t0 and t60/t0). Expression ratios were clustered using Rosetta software and Pearson correlation. Bar (top left corner) represents correlation of up- and down-regulation with the intensity of red and blue, respectively, on a log-10 scale.