Comparative Analysis of Ligand-Conserved, Species-Specific Gene Expression. (A) cDNA microarrays were used containing 13,361 mouse clones representing 8,734 unique genes and 8,507 rat clones representing 5,684 unique genes. There were 3,417 orthologous genes represented on the mouse and rat cDNA microarrays as determined by HomoloGene. (B) Differentially expressed genes were assessed for similar expression patterns using relaxed criteria (|fold change| > 1.3; P1(t) > 0.99) to minimize the likelihood of false-negatives that marginally failed to meet the selection criteria. (C) Common differentially expressed orthologous genes were examined for comparable expression patterns, and designated according to the coactivity categories (CAS, CAD, DAS, DAD) as described in Figure 3. The results were plotted on a coordinate correlation graph. A high proportion of differentially expressed orthologs exhibited a positive correlation when considering both fold-change and P1(t). (D) Comparisons of species-divergent (CAD) expression profiles identified 35 genes that were differentially expressed in the mouse and the rat but exhibited putative divergent regulation elicited by EE and TAM.