1. Each blue, red, or green dot represents the overall expression pattern of each AM sample from Normal, Dex, or Dex-Pc rats, respectively (Fig. 1). The PCA analysis showed that the samples within

each rat group were closely clustered together, whereas the samples between rat groups were distinctly separated, indicating that the quality of the microarray data was excellent. The PCA results also indicated that the global expression patterns in AMs of the same rat group were similar, whereas those in AMs of different rat groups were different. Figure 1 Principle component analysis of microarray results. The blue, red, and green oval PF-02341066 concentration dots represent linear PD0332991 chemical structure combinations of the expression data, including relative expression value

and variance, of the 8799 genes in AMs from each Normal, Dex, or Dex-Pc rat. The principle component analysis (PCA) software examined three components of genes in different samples for those with similar or different expression profiles. The first component, shown in the x-axis, includes genes with a high degree of variance. The second component, displayed in the y-axis, encompasses genes that had a median range of variance. The third component, represented by z-axis, contains those with a minor variance. Hierarchical clustering analysis of differentially expressed genes After ANOVA, 3473 genes were found to be differentially BAY 57-1293 cell line expressed due to dexamethasone treatment or Pneumocystis infection and were analyzed by hierarchical clustering using the Partek software (Fig. 2). Genes that were differentially expressed due to Pneumocystis infection were divided into four categories. The first one includes genes whose expressions were not affected by Pneumocystis infection. The second category includes those that were expressed at low levels but were up regulated by Pneumocystis infection. The third category contains genes that were expressed at high levels and were not affected by Pneumocystis infection. The fourth category includes those that were expressed at high levels but were down regulated by Pneumocystis infection. The same four

categories of gene expressions in AMs from dexamethasone treated rats were observed. Figure 2 Cytidine deaminase Hierarchical clustering of differentially expressed genes. ANOVA was first performed to identify genes that are differentially expressed due to dexamethasone treatment or Pneumocystis infection. Each lane represents the expression profile of AMs from one rat. The first four lanes show the expression profiles of AMs from the four Dex-Pc rats compared to that of Dex rats, the middle four lanes display those of the four Dex rats compared to that of Normal rats, and the remaining four lanes represent those of the four Dex-Pc rats compared to that of Normal rats. Red and blue colors indicate high and low expression levels, respectively. Gray color indicates no change in expression levels.