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Table 3 List of microarray features representing genes involved in nutrient metabolism that were differentially expressed in the liver of Atlantic salmon fed diets with different proportions of marine and terrestrial ingredients

From: Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed experimental diets based on terrestrial alternatives to fish meal and fish oil

Probe IDa

Best named BLASTx/BLASTn hit [species]b

Functional annotationc

ABP vs MARd

VEG vs MARd

VEG vs ABPd

Carbohydrate metabolism

 C035R008

Glucokinase ( gck ) [ Salmo marmoratus ]

P: glycolytic process

−2.4

−1.7

1.4

 C185R084

Predicted: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase isoform X2 ( pfkfb4 ) e [ S. salar ]

P: fructose metabolic process

−1.9

− 1.7

1.1

 C113R060

Predicted: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase isoform X2 ( pfkfb4 ) e [ S. salar ]

P: fructose metabolic process

−1.7

− 1.9

−1.1

 C043R025

Fructose-bisphosphate aldolase B [S. salar]

P: glycolytic process

− 1.4

−1.9

− 1.3

 C169R002

Predicted: 6-phosphogluconate dehydrogenase, decarboxylating ( 6pgd ) [ S. salar ]

P: pentose-phosphate shunt, oxidative branch

−1.3

−2.0

− 1.6

 C039R032

Predicted: 6-phosphogluconate dehydrogenase, decarboxylating ( 6pgd ) [ S. salar ]

P: pentose-phosphate shunt, oxidative branch

−1.0

−1.8

− 1.7

 C128R035

Predicted: glucose-6-phosphate 1-dehydrogenase-like (LOC106571947), transcript variant X3 [S. salar]*

P: pentose-phosphate shunt, oxidative branch

−1.1

−1.5

− 1.3

Lipid metabolism

 C134R089

Predicted: diacylglycerol O-acyltransferase 2-like (LOC106567948) ( dgat2b ) [ S. salar ]*

P: triglyceride biosynthetic process

−1.5

−2.7

− 1.8

 C103R066

Predicted: diacylglycerol O-acyltransferase 2 ( dgat2b ) [ S. salar ]

P: triglyceride biosynthetic process

−1.3

−2.0

− 1.6

 C050R151

Predicted: acetyl-CoA carboxylase isoform X7 ( acac ) [ S. salar ]

P: fatty acid biosynthetic process

−1.3

−2.4

− 1.8

 C086R144

Fatty acid-binding protein, heart ( fabp3 ) [ S. salar ]

P: long-chain fatty acid transport

1.2

−1.6

−1.9

 C262R025

Predicted: isopentenyl-diphosphate Delta-isomerase 1 isoform X1 ( idi1 ) [ S. salar ]

P: cholesterol biosynthetic process

1.7

1.9

1.1

 C130R156

Predicted: insulin-induced gene 1 protein-like [S. salar]

P: cholesterol biosynthetic process

2.4

1.6

−1.5

 C069R129

Fatty acyl-CoA reductase 1 [S. salar]

P: glycerophospholipid biosynthetic process

1.9

1.4

−1.4

 C078R087

Farnesyl pyrophosphate synthetase [S. salar]

P: cholesterol metabolic process

1.8

1.8

1.0

 C229R065

Predicted: squalene synthase isoform X2 ( sqs ) [ S. salar ]

P: cholesterol biosynthetic process

1.9

1.7

−1.1

 C025R006

Predicted: hydroxymethylglutaryl-CoA synthase, cytoplasmic-like (LOC106571543), transcript variant X4 [S. salar]*

P: cholesterol biosynthetic process

1.8

1.4

−1.3

 C067R143

Predicted: fatty acid hydroxylase domain-containing protein 2 [S. salar]

P: fatty acid biosynthetic process

−2.2

− 1.4

1.6

 C089R080

Predicted: apolipoprotein B-100 precursor [S. salar]

P: lipid transport

−1.6

− 1.3

1.2

 C190R063

Predicted: lipid phosphate phosphohydrolase 1 [S. salar]

P: lipid metabolic process

1.7

2.2

1.3

 C188R006

Predicted: long-chain-fatty-acid--CoA ligase ACSBG2 [S. salar]

P: long-chain fatty acid metabolic process

−1.7

−2.5

− 1.4

 C104R105

Predicted: adiponectin precursor [S. salar]

P: fatty acid beta-oxidation; P: glucose homeostasis

−1.5

−2.0

− 1.3

 C085R162

CCAAT/enhancer-binding protein alpha [S. salar]

P: lipid homeostasis; P:liver development

− 1.2

− 1.8

− 1.5

 C004R046

Predicted: fatty acid synthase [S. salar]

P: fatty acid biosynthetic process

−0.8

−1.3

−1.6

Nucleotide metabolism

 C098R022

Adenylosuccinate synthetase isozyme 1 C ( adssl1a ) [ S. salar ]

P: ‘de novo’ AMP biosynthetic process

− 1.9

−2.6

− 1.4

 C107R157

Predicted: adenylosuccinate synthetase isozyme 1 C-like (adssl1b)f [S. salar]

P: ‘de novo’ AMP biosynthetic process

−1.7

−2.5

− 1.5

 C016R136

Predicted: CTP synthase 1-like [S. salar]

P: ‘de novo’ CTP biosynthetic process

− 1.3

− 2.3

− 1.7

 C086R065

Predicted: kalirin-like isoform X6 [S. salar]

F: guanyl-nucleotide exchange factor activity

−1.2

1.7

2.0

  1. aRefers to the identifier of the probe on the 44 K array
  2. bThe contiguous sequences (contigs) from which the microarray probes were designed were used for gene identification by BLASTx against the NCBI nr database. The name of the protein [species] of the BLASTx hit with the lowest E-value (cutoff value of 10− 5) is presented. If no reliable BLASTx hits were found, the best BLASTn hit was chosen instead (E-value cutoff of 10− 10). BLASTn-identified genes are denoted with an asterisk. The names of those genes for which transcript levels were analyzed by real-time quantitative polymerase chain reaction (qPCR) are underlined. For the qPCR-analyzed genes, the gene symbol is indicated in brackets, differentiating paralogues if possible
  3. cGene ontology (GO) terms selected to functionally annotate the cDNA’s best BLASTx/BLASTn hit, obtained from putative Danio rerio and Homo sapiens orthologues (i.e., best BLASTx hit from these model species). GO terms were obtained from UniProt Knowledgebase. GO categories: biological process (P), molecular function (F), and cellular component (C)
  4. dFold-change (FC) values between two dietary treatments, calculated from microarray log2 ratios for a given probe (formula: 2A-B [55, 56]). Significant differences (PFP < 10%) between treatments are indicated by bolding the FC values
  5. eqPCR primers were designed based on a cDNA sequence for Salmo salar 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4-like (BT044025), which shares 100% identity with the 60mer microarray probes. See Additional file 2 for additional information regarding BLASTx/BLASTn statistics and identity among the nucleotide sequences used for designing the microarray and qPCR probes
  6. fAdssl1a and adssl1b paralogues showed 93% identity over 597 aligned nucleotides (see Additional file 3). Paralogue adssl1b was not qPCR-analyzed because none of the designed primer pairs passed quality testing due to low transcript levels (i.e., 10 ng of input total RNA yielding Ct values above 31)
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BMC Genomics

ISSN: 1471-2164

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