## 3 Results
### Microarray Analysis  
The Pearson correlation of all genes showed that the gene expression profile was similar through all of the rainbow trout specimens used in the experiment (average R = 0.71, \(p\)-value \(<\) 0.05; Figure 2). In this study, the limma and RankProd packages in R were used to identify the DEGs among the samples (FC \(>\) 2, \(p\)-value \(<\) 0.05; Supplementary Table S1). In total, 656 and 434 genes showed statistically different expressions after 2 and 6 days of infection, respectively (Figure 3a,b). Of these, 382 and 221 were up-regulated, and 274 and 213 were down-regulated at 2 dpi and 6 dpi, respectively (Figure 3a,b). On average, 98.05% of the DEGs were annotated using NCBI nr databases (excluding uncharacterized, unnamed and hypothetical proteins), and gene symbols using Zfin and HGNC databases were assigned to 92.58% of them. Further, using Blast2 GO software (version 6.0.3), gene ontology (GO) terms were assigned to 76,58% of the annotated DEGs and they were classified into three main categories: biological processes, molecular function and cellular component (Supplementary Table S1). In the moribund group, the highly expressed genes belonged to the cytokine-cytokine receptor interaction pathway, such as _cd209_, the c-type lectin domain family 4 member e (_clecde_), interleukin 11 (_il11_) and potassium channel tetramerization domain-containing 12 gene (_kctd12_), which is involved in ion transport. In the fish that survived, the highly expressed genes were related to lipid metabolism, such as mid1 interacting protein 1 (_mid1 ip1_) and matrix metalloproteinase 13 (_mmp13_), which is involved in collagen degradation. In both groups, a gene encoding calcium-binding protein and  
Figure 1: Immunoassay analysis of infected fish: 2 dpi (moribund, n = 4), 6 dpi (survivors, n = 3) and uninfected (control, n = 3). Statistical comparison was carried out using Kruskal–Wallis test. (**a**) Ceruloplasmin activity in the plasma. (**b**) Gamma globulin level in the serum. (**c**) Lysozyme activity in the plasma. Significant differences are indicated by different lowercase letters (\(p\)-value \(<\) 0.05); same letter indicates no statistical difference. coiled-coil domain 1 (_calcoco1_) were highly increased (Figure 3a,b). On the other hand, in the 2 dpi group, the down-regulated genes were the immune-related c-c motif chemokine ligand 13 (_cc113_), liver enriched antimicrobial peptide 2 (_leap2_) and c1q and tnf-related 3 (_ctrp3_). In the 6 dpi group, the genes with the lowest expressions were s100 calcium-binding protein p (_s100p_), cathepsin (_cts11_) and MHC class I heavy chain. In both groups, the heavily reduced genes were heat shock protein 90 alpha family class a member 1 (_lsp90 aa1_) and inositol 1,4,5-trisphosphate receptor type 2 (_itpr2_), which is involved in cell cycle and calcium transport (Figure 3a,b). Figure 3: Volcano map of differentially expressed genes (DEGs) in (**a**) moribund fish (2 dpi group) and (**b**) survivor fish (6 dpi group). Red color represents up-regulated genes, whereas blue color shows down-regulated genes. Grey color shows non-significant genes. Differentially expressed genes were identified based on fold change (FC) > 2 (FC(log2) > 1 on _x_-axis) and significance(\(-\)log\({}_{10}\)) over 1.3 (_y_-axis), which represents _p_-value < 0.05. Gene symbols are presented for top five DEGs with highest and lowest expression values in each experimental group. Gene symbols: liver-enriched antimicrobial peptide 2 (_leap2_), c-c motif chemokine ligand 13 (_cc113_), inositol 1,4,5-trisphosphate receptor type 2 (_itpr2_), c1q and tnf-related 3 (_ctrp3_), heat shock protein 90 alpha family class a member 1 (_lsp90 aa1_), cd209 molecule (_cd209_), c-type lectin domain family 4 member e (_clec4e_), ion transport  
Figure 2: Pearson correlation coefficient analysis between infected fish, presented as matrix graphic (RT1, RT2, RT3 and RT4 were moribund, whereas RT5, RT6 and RT7 were survivor fish). All samples showed positive correlation.