Table 3

Liver transcripts differentially expressed when examining the explanatory power of the variable 'total lipid' level in flesh of four families of Atlantic salmon fed the same low FM/high VO diet
Probe name Gene High/Low Lipid p-value
Lo LC-PUFA (HL/LL) Hi LC-PUFA (HH/LH)
Metabolism (30%)
Lipid metabolism (8%)
Ssa#STIR02479 Butyrophilin subfamily 2 member A2 precursor 7.76 1.23 0.0001
Ssa#STIR03356 Acyl carrier protein, mitochondrial precursor - 5.17 - 1.55 0.0004
Ssa#STIR00151_3 Polyunsaturated fatty acid elongase (elovl2) - 1.40 - 1.87 0.0190
Ssa#STIR00151_2 Polyunsaturated fatty acid elongase (elovl2) - 1.28 - 1.97 0.0238
Con_CANDS_03 Polyunsaturated fatty acid elongase (elovl2) - 1.33 - 1.82 0.0310
Ssa#STIR24266 Acyl carrier protein, mitochondrial precursor - 2.88 - 1.52 0.0312
Ssa#STIR21802 Stearoyl-CoA desaturase 3.53 3.17 0.0324
Ssa#STIR00151_4 Polyunsaturated fatty acid elongase (elovl2) - 1.41 - 1.82 0.0393
Ssa#S35501441_S Acyl carrier protein, mitochondrial precursor - 2.65 - 1.44 0.0457
Ssa#KSS4634 Stearoyl-CoA desaturase 3.52 2.82 0.0486
Energy metabolism and generation of precursor metabolites (11%)
Ssa#S31995754 Cytochrome c oxidase subunit 2 6.57 - 1.12 0.0002
Ssa#STIR03496 LYR motif-containing protein 5 1.20 1.48 0.0233
Ssa#STIR03740 6-Phosphogluconate dehydrogenase, decarboxylating 1.60 1.93 0.0238
Ssa#TC106663 Creatine kinase, testis isozyme 1.76 1.46 0.0380
Ssa#STIR19155 NADH dehydrogenase iron-sulfur protein 7 1.21 2.30 0.0409
Ssa#STIR12872 V-type ATPase B subunit - 1.19 - 1.24 0.0419
Protein and amino acid metabolism (4%)
Ssa#STIR03710 Proteasome subunit beta type-9 precursor 1.94 25.52 0.0001
Ssa#S30294677 Serine protease HTRA1 precursor (Serine protease 11) 3.42 2.44 0.0089
Carbohydrate metabolism (4%)
Ssa#TC106766 Glycogenin 8.64 1.67 0.0093
Ssa#S30290426 Serine dehydratase-like 1.60 1.72 0.0393
Xenobiotic and oxidant metabolism (4%)
Ssa#S35671757 Extracellular superoxide dismutase 2.18 1.09 0.0061
Ssa#STIR25620 Microsomal glutathione S-transferase 1 2.45 2.72 0.0096
Omy#S18159333 Microsomal glutathione S-transferase 1 2.47 3.15 0.0233
Transport (2%)
Ssa#S35599996 ATPase, H + transporting, lysosomal, V1 subunit H 45.10 15.16 0.0000
Translation (4%)
Ssa#STIR26031 Mitochondrial 28 S ribosomal protein S34 1.19 19.22 0.0000
Ssa#S30241612 39 S ribosomal protein L16 1.30 1.51 0.0324
Regulation of transcription (12%)
Ssa#STIR06878 Cytosolic iron-sulfur protein assembly 1 - 1.16 - 1.56 0.0106
Ssa#TC112002 Retinoid X receptor beta 1.20 - 16.00 0.0254
Omy#S15320037 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a4 - 1.97 - 1.53 0.0324
Ssa#CN181280 alpha thalassaemia mental retardation X-linked protein - 3.05 - 6.90 0.0419
Ssa#S35697153 YLP motif containing 1 - 1.49 - 1.32 0.0428
Ssa#S35486480 Zinc finger protein 492 - 1.08 - 2.29 0.0452
Signalling and protein modification (13%)
Ssa#STIR15776 Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 4 - 84.27 2.44 0.0000
Ssa#STIR23530 Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 4 - 83.34 2.60 0.0000
Ssa#STIR03642 Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 4 - 49.76 2.34 0.0001
Ssa#STIR01857 Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 4 - 74.19 2.51 0.0011
Ssa#S35516167 14 kDa phosphohistidine phosphatase 1.57 1.34 0.0019
Ssa#STIR11086 Lunatic fringe - 5.47 - 2.00 0.0154
Ssa#S30263209 HtrA serine peptidase 3 3.71 2.33 0.0154
Ssa#STIR22920 HCLS1-associated protein X-1 1.73 2.33 0.0390
Ssa#S35701148 Phosphatase and actin regulator 3 - 1.52 - 65.53 0.0404
Omy#S15290792 Serine/threonine-protein kinase PLK2 1.70 2.03 0.0468
Immune response (29%)
Ssa#STIR00130_4 Complement factor H precursor (cfh) - 1.43 - 1.67 0.0012
Ssa#S35536179 novel NACHT domain containing protein - 1.89 - 2.41 0.0013
Ssa#S30241035 MHC class I - 1.55 - 30.59 0.0024
Ssa#S35516341 Tripartite motif-containing protein 25 (trim25) - 5.64 - 4.34 0.0125
Ssa#S18834140 Complement factor H precursor (cfh) - 1.34 - 1.57 0.0131
Omy#utu04b09 Complement factor H precursor (cfh) - 1.56 - 1.70 0.0134
Ssa#STIR15577 Tissue factor pathway inhibitor a 21.03 1.59 0.0151
Ssa#S35558236 C-type lectin domain family 16, member A 4.59 2.25 0.0190
Ssa#STIR10409 CD83 antigen precursor 1.98 1.68 0.0238
Omy#S15332652 Putative pentraxin - 1.33 159.84 0.0246
Ssa#S35685271 GTPase IMAP family member 7 −168.44 - 4.09 0.0263
Ssa#S35551959 Duodenase-1 - 2.94 - 2.77 0.0349
Ssa#S35558945 Tripartite motif-containing protein 25 (trim25) - 5.74 - 4.28 0.0373
Ssa#S35685273 Lactose-binding lectin l-2 precursor putative 1.56 4.04 0.0380
Ssa#S31977617 Scavenger receptor cysteine-rich type 1 protein m130 - 1.31 - 2.05 0.0404
Ssa#STIR04893 Lactose-binding lectin l-2 precursor putative 1.57 4.15 0.0419
Ssa#S30264865 Indoleamine-pyrrole 2,3-dioxygenase 2.83 1.06 0.0444
Ssa#S31981622 Granzyme A - 5.31 - 4.33 0.0444
Ssa#S35685718 CD83 antigen precursor 2.03 1.58 0.0462
Ssa#KSS3969 Leukocyte cell-derived chemotaxin 2 precursor (lect2) 3.16 4.86 0.0486
Structural proteins (10%)
Ssa#STIR03004 Troponin I, slow skeletal muscle - 202.28 - 135.03 0.0000
Ssa#CK891024 Vitelline envelope protein gamma 1.07 - 15.43 0.0002
Ssa#STIR02053 Troponin I, slow skeletal muscle - 70.21 - 10.07 0.0005
Omy#S34312003 similar to Titin (Connectin) - 44.29 - 29.86 0.0013
Omy#S15317515 Type I keratin E7 5.08 2.43 0.0167
Ssa#STIR05140 Troponin I, slow skeletal muscle - 13.16 - 14.20 0.0124
Ssa#STIR08802 Myosin regulatory light chain 2, smooth muscle isoform 1.55 1.34 0.0324
Miscellaneous/unknown function
Ssa#S35519407 Tetratricopeptide repeat protein 23 3.64 1.02 0.0012
Ssa#S35584894 NCK-associated protein 1-like - 1.82 - 1.70 0.0019
Ssa#S35521859_S FAM36A 1.11 5.75 0.0047
Ssa#STIR02307 FAM36A 1.16 3.31 0.0058
Ssa#TC87798 Envelope polyprotein - 1.83 - 1.03 0.0233
Ssa#STIR20319 TPA-induced transmembrane protein - 1.09 1.75 0.0233
Ssa#TC110493_S Beta-3-galactosyltransferase 6.80 1.80 0.0233
Ssa#S30270166 Transmembrane protein 37 2.13 1.90 0.0254
Ssa#STIR08658 Tetraspanin-3 putative - 3.20 - 1.47 0.0312
Ssa#S30293470 Deoxyribonuclease gamma precursor 2.19 2.85 0.0366
Ssa#S35667723 Dynein, cytoplasmic 1, light intermediate chain 2 - 1.90 - 1.48 0.0366
Ssa#CX354464 Retinol dehydrogenase 12 2.37 2.35 0.0373
Ssa#S35582016 Type I iodothyronine deiodinase 1.51 1.74 0.0380
Ssa#S35515630 C7orf57 1.32 1.13 0.0380
Ssa#STIR15617 FAM36A 1.02 4.60 0.0403
Ssa#STIR31448 osteopontin-like - 4.84 - 1.58 0.0419
Ssa#STIR26263 Anterior gradient protein 2 homolog precursor 3.72 1.68 0.0419
Ssa#TC65497_S Adipocyte plasma membrane-associated protein 2.50 1.64 0.0419
Ssa#TC93681 Ring finger protein 44 - 1.23 - 1.17 0.0455
Ssa#EG819142 Glutaminyl-peptide cyclotransferase-like - 1.11 - 1.49 0.0455

Results were obtained by two-way ANOVA analysis (p < 0.05; fold change cut-off of 1.2) with Benjamini-Hochberg multiple testing correction. Transcripts (109 probes; 18% unknowns) are arranged by categories of biological function and, within these, by p-value. Indicated are also the probe names and the expression ratio determined separately between families with high vs low total lipid level, for each n-3 LC-PUFA grouping. Percentages of distribution of genes within each category do not include non-annotated probes, those representing the same gene or with a miscellaneous function.

Morais et al.

Morais et al. BMC Genomics 2012 13:410   doi:10.1186/1471-2164-13-410

Open Data