Table 2

Liver transcripts differentially expressed when examining the explanatory power of the factor 'n-3 LC-PUFA' content in flesh of four families of Atlantic salmon fed the same low FM/high VO diet
Probe name Gene High/Low LC-PUFA p-value
L Lipid (LH/LL) H Lipid (HH/HL)
Metabolism (21%)
Energy metabolism (4%)
Ssa#S31995754 Cytochrome c oxidase subunit 2 7.1 - 1.0 0.0001
Protein and amino acid metabolism (13%)
Ssa#CB502423 N-acetylated alpha-linked acidic dipeptidase-like 1 3.7 79.8 0.0011
Ssa#STIR03710 Proteasome subunit beta type-9 precursor - 14.9 - 1.1 0.0026
Ssa#S31993738_S Ubiquitin-conjugating enzyme E2 - 3.3 - 1.4 0.0188
Xenobiotic and oxidant metabolism (4%)
Ssa#S18892279 Cytochrome P450 1A 1.8 1.4 0.0096
Ssa#STIR00161_2 Cytochrome P450 1A 1.9 1.4 0.0160
Ssa#STIR00161_3 Cytochrome P450 1A 2.5 1.8 0.0213
Con_CANDS_13 Cytochrome P450 1A 2.0 1.4 0.0494
Translation (8%)
Ssa#STIR26031 Mitochondrial 28 S ribosomal protein S34 - 11.1 1.5 0.0017
Ssa#S18867312 Ribonuclease UK114 1.4 1.4 0.0450
Regulation of transcription (17%)
Ssa#S35510106 Zinc finger protein 367 - 1.4 6.5 0.0026
Omy#S18104058 Zinc finger protein 235 4.1 2.3 0.0058
Ssa#TC111702 Reverse transcriptase-like protein - 1.3 4.6 0.0104
Ssa#TC112002 Retinoid X receptor beta 1.0 - 19.1 0.0134
Signalling and protein modification (17%)
Ssa#STIR15776 Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 4 - 1.7 123.3 0.0000
Ssa#STIR23530 Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 4 - 1.9 115.6 0.0000
Ssa#STIR03642 Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 4 - 1.7 68.1 0.0000
Ssa#STIR01857 Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 4 - 1.5 125.5 0.0001
Ssa#STIR31840 Sphingomyelin phosphodiesterase acid transcript variant 1 2.1 2.3 0.0303
Ssa#STIR07369 RAF1 proto-oncogene serine/threonine-protein kinase 1.8 1.3 0.0343
Ssa#S35552908 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide - 1.6 - 2.1 0.0455
Immune response (38%)
Ssa#S35536179 similar to novel NACHT domain containing protein 2.4 1.8 0.0026
Ssa#S35516341 Tripartite motif-containing protein 25 (trim25) 5.2 6.7 0.0066
Ssa#S30241035 MHC class I - 1.3 - 26.0 0.0079
Ssa#STIR02298 c-c motif chemokine 13 precursor (ccl13) 4.4 3.0 0.0100
Ssa#S35581943 Myelin and lymphocyte protein (mal) - 22.2 - 25.0 0.0100
Ssa#KSS3969 Leukocyte cell-derived chemotaxin 2 precursor (lect2) 4.6 7.1 0.0134
Ssa#STIR15577 Tissue factor pathway inhibitor a 22.3 1.7 0.0135
Omy#S15332652 Pentraxin - 1.1 199.4 0.0172
Ssa#TC70262 Cathepsin K 1.4 2.3 0.0279
Ssa#S35558945 Tripartite motif-containing protein 25 (trim25) 4.8 6.5 0.0347
Miscellaneous/unknown function
Ssa#STIR09736 Transmembrane protein 42 2.3 1.9 0.0009
Ssa#S35519407 Tetratricopeptide repeat protein 23 3.7 1.0 0.0011
Ssa#STIR02307 Family with sequence similarity member a (FAM36A) 1.3 3.6 0.0026
Omy#BX309274 X-ray repair complementing defective repair in Chinese hamster cells 3 - 1.0 - 8.0 0.0100
Ssa#STIR21287 Solute carrier family 30 (zinc transporter) member 7 2.1 1.5 0.0100
Ssa#S35521859_S Family with sequence similarity member a (FAM36A) - 1.1 4.8 0.0358
Ssa#S18842295 Alveolin 1.7 4.6 0.0422

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 (43 probes; 12% 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 n-3 LC-PUFA contents, for each total lipid level. 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

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