Microarray analysis of the Ser585-survival pathway. CTL-EN cells expressing either wild-type βc or the βcSer585Gly mutant were factor deprived for 18 hours and then stimulated with GM-CSF for 0, 12, and 18 hours. Total RNA was isolated, reverse transcribed, and labeled; cDNA was used to probe either NIA 15k cDNA or AMF 21K microarrays. Pairwise comparisons were performed as in panel A whereby each solid arrow represents a separate 15k cDNA slide (n = 14) and each dotted arrow represents a 21k oligonucleotide slide (n = 8) in which differential gene expression was examined in either (1) cells expressing the wild-type βc or the βcSer585Gly mutant at a single time point or (2) a single cell line at different time points. Microarray data were subjected to Bayesian analysis to identify genes that were differentially expressed in CTL-EN cells expressing the wild-type βc and βcSer585Gly mutant in response to GM-CSF at 12 hours (B) and 18 hours (C). Bayesian analysis is shown whereby the probability that a particular gene is differentially expressed (t statistic) is plotted against the magnitude (log₂ scale) of the differential expression (interaction coefficient) for each gene represented on the cDNA array. Negative interaction coefficients correspond to genes that are more strongly expressed in cells expressing the wild-type βc than the βcSer585Gly mutant (eg, genes that are induced by GM-CSF in cells expressing the wild-type βc and not in the βcSer585Gly mutant). Positive interaction coefficients correspond to genes that are more strongly expressed in cells expressing the βcSer585Gly mutant than the wild-type βc (eg, genes that are repressed by GM-CSF in cells expressing the wild-type βc and not in the βcSer585Gly mutant). Selected genes identified by GO analysis in Figure 3 as having a role in cell survival or cytokine signaling and that also showed differential expression are highlighted. (D-E) Microarray data presented as the response in wild-type βc cells (M = log₂ [fold change in response to GM-CSF in CTL-EN cells expressing the wild-type βc]) plotted against the response in the βcSer585Gly mutant cells (M = log₂ [fold change in response to GM-CSF in CTL-EN cells expressing the βcSer585Gly mutant]). Although most genes are either not GM-CSF regulated (M values close to 0 for both wild-type βc and βcSer585Gly mutant) or are GM-CSF regulated in an equivalent manner in cells expressing the wild-type βc and βcSer585Gly mutant (M values lie close to the diagonal line), a restricted subset lies off the diagonal. The M values for the genes highlighted in panels B to E at 0, 12, and 18 hours were plotted for cells expressing either the wild-type βc (○) or the βcSer585Gly mutant (Δ) (F). (G) A clustered heat map of the 138 genes identified as being differentially expressed between the wild-type βc and βcSer585Gly mutant CTL-EN cells in response to GM-CSF was generated with the use of a Euclidean matrix. The M value (log₂ fold change) for both CTL-EN cells expressing the wild-type βc or the βcSer585Gly mutant was converted to a color scale with red indicating that the gene is induced by GM-CSF, green indicating that the gene is repressed, and the color intensity indicating the magnitude of regulation.