Table 6

Genes significantly different in skeletal muscle of fish PP diet
Probe name1 ACC2 FC ± SEM3 Identity4
Immune function
Ssa#STIR12634 TC70300 5.0 ± 1.2 Vig-2
Ssa#STIR00067_2 U66477 3.2 ± 1.3 Interferon inducible Mx protein
Ssa#CK894557 CK894557 −11.2 ± 1.4 MHC class Ib antigen
Ssa#STIR00132_2 NM_001140254 −7.4 ± 1.3 Tumor necrosis alpha-induced protein 2
Omy#NP565601 NP565601 −6.4 ± 1.4 T-cell receptor beta
Ssa#S31982089 S31982089 −5.4 ± 1.1 Platelet-activating factor receptor
Ssa#STIR12498 TC70105 −4.6 ± 1.2 γ-ip (CXCL10)
Ssa#S48440415 S48440415 −3.4 ± 1.1 SMAD3
Omy#S15331473 S15331473 −3.2 ± 1.2 Interferon-inducible protein Gig2-like
Ssa#S35544087 S35544087 −3.1 ± 1.3 B-cell CLL/lymphoma 7 protein family member B
Ssa#STIR13083 TC70912 −3.6 ± 1.0 SAMHD1
Omy#S18153399 S18153399 −2.4 ± 1.1 CD80
Ssa#KSS5035 KSS5035 −2.2 ± 1.2 Interferon regulatory factor 2-binding protein
Ssa#STIR00071_3 DW580947 −2.3 ± 1.1 Interferon -induced protein 35
Ssa#STIR08451 TC64790 −2.2 ± 1.2 Heat shock protein 47
Ssa#S35480903 S35480903 −2.0 ± 1.2 Heat shock protein 30
Ssa#STIR29454 TC95297 −2.1 ± 1.1 Beta defensin 1
Cell proliferation and apoptosis
Ssa#S35602638 S35602638 3.7 ± 1.4 Tripartite motif 39
Ssa#TC110067 TC110067 3.5 ± 1.5 Cell death inducing protein
Ssa#STIR08668 TC65039 3.1 ± 1.1 Bh3 interacting domain death agonist
Ssa#STIR12507 TC70118 3.0 ± 1.3 Syndecan 4
Ssa#STIR02208 BT049868 −38.6 ± 1.2 Caspase 14
Ssa#S35559333 S35559333 −4.1 ± 1.3 Ankyrin repeat domain-containing protein 54
Omy#TC151190 TC151190 −2.9 ± 1.2 Nucleostemin
Ssa#S35550715 S35550715 −2.8 ± 1.2 Growth hormone-inducible transmembrane protein
Ssa#S35585784 S35585784 −2.6 ± 1.1 Caspase-8
Ssa#KSS5035 KSS5035 −2.4 ± 1.2 Interferon regulatory factor 2-binding protein 2-B
Protein metabolism
Ssa#S35682089 S35682089 4.2 ± 1.3 Ubiquitin-like protein 1
Ssa#STIR17445 TC77227 2.6 ± 1.3 Acta1 protein
Ssa#STIR21465 TC83266 2.5 ± 1.2 Actin-binding
Ssa#STIR03710 BT048358 2.0 ± 1.2 Proteasome subunit beta type-9
Ssa#STIR00115_4 BT045917 2.0 ± 1.2 Tropomyosin-1 alpha chain
Ssa#S32008331 S32008331 −3.6 ± 1.7 40 S ribosomal protein S16
Ssa#CL224Ctg1 NM_001140473 −2.8 ± 1.5 Receptor-interacting serine/threonine-protein kinase 4
Omy#CX150460 CX150460 −2.7 ± 1.1 60 S ribosomal protein L27
Omy#S15320960 S15320960 −2.6 ± 1.1 Cathepsin D
Ssa#TC111443 TC111443 −2.5 ± 1.1 Serine/threonine-protein kinase 35
Ssa#FC072705 FC072705 −2.3 ± 1.0 40 S ribosomal protein S10
Ssa#S35583213 S35583213 −2.1 ± 1.2 Serine/threonine-protein kinase PINK1
Ssa#S35591236 S35591236 −2.1 ± 1.1 Histidine triad nucleotide-binding protein 3
Energy metabolism
Ssa#STIR39924 TC110855 2.5 ± 1.1 Cytochrome P450
Ssa#S32006874 S32006874 2.2 ± 1.1 Peroxisomal membrane protein 11 C
Ssa#KSS5038 KSS5038 −4.0 ± 1.3 Phosphoglycerate kinase
Ssa#STIR19484 TC80264 −3.1 ± 1.3 Cytochrome c oxidase polypeptide viii
Ssa#CL200Ctg1 BT059338 −2.8 ± 1.3 L-lactate dehydrogenase B chain
Ssa#S30282925 S30282925 −2.7 ± 1.1 Peroxisomal 3.2-trans-enoyl-CoA isomerase
Omy#CX150319 CX150319 −2.4 ± 1.2 Cytochrome c oxidase subunit II
Ssa#STIR13627 TC71700 −2.1 ± 1.2 Cox18 cytochrome c oxidase
Ssa#EL698167 EL698167 −2.0 ± 1.1 Malate dehydrogenase 1

List of selected mRNAs found to be higher or slower in expression following the feeding trial in mid intestine (a), liver (b) or skeletal muscle (c) and grouped according to functional classes (shown in bold). The selection was based on manual assignment of function and 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 and greater than 2-fold change. 1Indicates the unique code for the feature on the microarray, 2Accession number of the cDNA sequence. 3Fold-change for genes higher or lower expressed in fish fed PP relative to fish fed MP diet. 4Identity of the probe target as determined by BLASTX and BLASTN searches.

Tacchi et al.

Tacchi et al. BMC Genomics 2012 13:363   doi:10.1186/1471-2164-13-363

Open Data