## 3 Results
### Microarray Analysis
Color and size of circles (light blue to dark blue) indicate rising correlation value. potassium channel tetramerization domain containing 12 gene (_kctd1_), interleukin 11 (_i111_), calcium binding and coiled-coil domain 1 (_calcoco1_), s100 calcium binding protein p (_s100p_), cathepsin (_cts1I_), MHC class I heavy chain (_mhc1_), mid1 interacting protein 1 (_mid1 ip1_), matrix metallopeptidase 13 (_mmp13_) and polyubiquitin 11 (_ub11_). A comparison between the moribund (2 dpi) and survivor groups (6 dpi) using a Venn diagram revealed that only 24.71% and 22.06% of the gene symbols and probe names were shared between the groups (Figure 4a,b). Moreover, the Wilcoxon rank sum test using the absolute value of the log2 FC revealed that the median expression was significantly different between the studied groups, and it was greater in the moribund fish compared to the survivor fish (_p_-value < 2.2 \(\times\) 10\({}^{-16}\)). Based on gene symbols, a pathway and GO enrichment analysis was performed (Figure 5a,b; Supplementary Figures S1 and S2; _p_-value < 0.001). A comparison between the identification numbers (IDs) revealed that 27.93% of the up-regulated pathways and 32.83% of the down-regulated pathways were shared between the moribund and survivor groups. The obtained results revealed that an infection with _A. salmonicida_ increased the immune system response (c-type lectin receptor signaling pathway, cytokine-cytokine receptor interaction, il-17 signaling pathway and neutrophil degranulation), apoptosis, autophagy and collagen degradation in both the moribund and survivor fish. Further, the cellular senescence, chemokine signaling pathway, complement and coagulation cascades, ferrotosis, fc gamma r-mediated phagocytosis and the foxo signaling pathway were uniquely enriched at 2 dpi. After 6 days post infection, the fatty acid metabolism, DNA repair, programmed cell death, MHC class II antigen presentation, intrinsic pathway for apoptosis and the citric acid (TCA) cycle and respiratory electron transport were enriched. The pathways involved in collagen degradation and formation, glycolysis/gluconeogenesis, extracellular matrix organization and protein digestion and absorption were decreased in both of the infected groups. Further, in the 2 dpi group, genes involved with the cell cycle, DNA replication and ECM receptor interaction were down-regulated, whereas apoptosis, vitamin digestion and absorption, glycine, serine and threonine metabolisms and ion channel transport were decreased in 6 dpi. To identify the differentially expressed genes between groups, the limma package was used. An analysis revealed 169 DEGs, of which 76 increased over time and 93 decreased over time (Figure 6a, Supplementary Table S2). To present the relationship between the samples, hierarchical clustering was carried out using all of the identified genes (169 DEGs; Figure 6b). Genes such as cerebellum 1 (_cbln1_; FC = 19.26), complement c1q-like protein 2 (_c1q2_; FC = 17.49), proteasome subunit beta type-7 (_psmb7_; FC = 17.22), c-type lectin domain family 4 member e (_cletc4e_; FC = 17.21) and proteasome subunit beta type-8 (_psmb8_; FC = 8.42) significantly decreased over time. On the other hand, the expressions of c1q and tnf-related 3 (_ctrp3_; FC= 5.03), interferon-inducible protein gig2 (_gig2p_; FC = 4.92), myelin  
Figure 4: (**a**) Venn diagram of shared gene symbols between moribund and survivor fish (2 dpi vs. 6 dpi). (**b**) Venn diagram of shared probe names between moribund and survivor fish (2 dpi vs. 6 dpi). and lymphocyte protein-like (_mal_; FC = 4.52), cytochrome c (_cyc_; FC = 4.35) and keratin type I cytoskeletal 13 (_krt13_; FC = 3.63; Supplementary Table S2) increased over time.