a) 3-D view of PCA scores plot of Ido1 −/− group (n = 3) versus Ido1 +/+ group (n = 3). Groups are shown by different colors and dots represent individual strains. Blue spots represent Ido1 +/+ group and the red spots represent Ido1 −/− group. On a 3D-PCA plot of Ido1 −/− group can be clearly distinguished from Ido1 +/+ group. ( b) Hierarchical clustering and heat map of up- or down-regulated genes that are differentially expressed (>2-fold, 1% [FDR]) in the absence of IDO1. Red indicates high relative expression and green indicates low expression of genes as shown in the scale bar. Cluster analysis functionally categorized by IPA; Canonical pathway significantly detected in Ido1 −/− mice compared to Ido1 +/+ mice. Statistical significance of pathway modulation was calculated via a right-tailed Fisher’s exact test in Ingenutity Pathway. ( c, d) Gene-pathway networks using IPA. ( c) Gene Expression and ( d) Inflammatory Response pathway are displayed as networks. Green and red symbols denote down-regulated and up-regulated genes in Ido1 −/− compared with Ido1 +/+ mice, respectively. Arrows with unbroken lines indicate a direct interaction between two molecules, with the mode of action in the direction of the arrow; arrows with broken lines denote an indirect interaction. ( e) We performed gene-set-enrichment analysis (GSEA) to determine whether the filtered gene list from Ido1 −/− mice versus Ido1 +/+ mice showed specific enrichment in the inflammatory response in the rank-based analysis. Rank of 102 genes in our data sets ordered by expression level with enrichment plots for the up-regulated and down-regulated genes. ES (Enrichment Score) is a value that represents how well the gene set is enriched within the selected gene list. The FDR q value <0.01 for specific enrichment of the gene set is as indicated. The leading edge analysis of our microarray data identified that the gene is highly correlated with Inflammatory Response.