Table 2. Differentially regulated genes indicative of the non-protective/pathological response to Y. ruckeri infection.

cDNA microarrayprobe Acc. No.	cDNA microarrayUI72h vs UU (FC)	Real-time PCR UI72h vsUU (FC)	BLAST identification
EG852527	34.4 ↑	47.1 ↑	Cathelicidin (asCATH2)
CB511230	18.0 ↑	47.1 ↑	Cathelicidin antimicrobial peptide (asCATH2)
CB511048	6.4 ↑	19.5 ↑	C-type lectin domain family 4 member E
CK990871	6.3 ↑	16.7 ↑	Collagenase 3 precursor
CA046376	5.2 ↑	48.8 ↑	AF281355_1 differentially regulated trout protein 1
CA038364	3.9 ↑	NA	Cytochrome b-c1 complex subunit 9
EG845905	2.9 ↑	NA	45217 pfam05316, Mitochondrial ribosomal protein

The differential regulation of genes at 72 h post-challenge in unvaccinated fish (UI72h) compared to uninfected unvaccinated fish (UU) was considered a non-protective/pathological response to Y. ruckeri infection as 83% of the group of fish in which these genes were identified died by 21 d post-challenge. Arrows indicate the direction of the fold change while NA indicates genes not assessed by real-time PCR.