Inflammatory responses in primary muscle cell cultures in Atlantic salmon (Salmo salar)

BMC Genomics

Table 3 Differential expression of genes related to proteolysis

Gene ID¹	Annotation²	Mean fold change± SE³	Identity⁴
Ssa#CL13Contig1	CL13Contig1	10.0 ± 1.8	Collagenase 3
Ssa#S30266930	DW553898	8.3 ± 0.4	Angiotensinogen
Ssa#CK884742	CK884742	3.4 ± 0.5	Cytosolic non-specific dipeptidase
Ssa#S35528810	EG815188	3.2 ± 0.1	Ubiquitin-like protein 1
Ssa#S18890005	CB515535	2.8 ± 0.2	E3 ubiquitin-protein ligase RNF144A-A
Ssa#DW564916	DW564916	2.7 ± 0.4	Ubr5 protein
Ssa#CL300Ctg1	CL300Contig1	2.4 ± 0.1	Proteasome subunit beta type-6 precursor
Ssa#KSS4965	KSS4965	2.3 ± 0.1	Proteasome subunit beta type 7b
Ssa#STIR04015	BT048053	2.2 ± 0.1	Proteasomebeta type 8
Ssa#S30295323	DW582287	2.2 ± 0.1	Proteasome subunit alpha type-6
Ssa#S35509463	EG795841	2.0 ± 0.0	E3 ubiquitin-protein ligase CHFR
Ssa#S35533557	EG819935	−2.1 ± 0.1	Ubiquitin-conjugating enzyme E2 T
Ssa#S35507555	EG793933	−2.1 ± 0.2	Calpain small subunit 1
Ssa#S35530808	EG817186	−2.1 ± 0.1	Cystatin-B
Ssa#S31992074	DY720671	−3.8 ± 0.2	Ubiquitin- containing phd and ring finger 1
Ssa#S30242447	NM_001141717	−3.9 ± 0.2	Serine protease htra1
Ssa#S35564994	EG851372	−16.2 ± 0.9	Protease, serine, 35

List of selected mRNAs related to proteolysis found to be increased or decreased in expression in response to rIL-1β stimulation. Genes were assigned to the table based upon both their GO identifier and previous knowledge of their functions. Genes with greatest fold differences in expression are presented, the genes that are lower in expression are denoted by (-) value. The genes shown were significant at p < 0.05 following t- tests with Benjamini-Hochberg FDR and greater than 2-fold change. ¹Indicates the unique code for the feature on the microarray, ² Accession number of the cDNA sequence, accession numbers beginning with TC are for oligos from the TIGR Atlantic Salmon Gene Index. ³Fold change, in the case of oligos that featured multiple times in the gene list the one with the highest fold change is reported. ⁴Identity of the probe target as determined by BLASTX and BLASTN searches.

ISSN: 1471-2164