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Table 2 Functional annotation and fold change (FC) transcript expression for 41 qPCR genes

From: The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

Gene Symbola

Gene Namea

Functional Themeb

Key Function (UniProt)c

FC WNd

FC WHe

Genes Related to Heat Shock Response

 hsp70

Heat shock protein HSP 70

Heat Shock Response (#1)

MF: Chaperone, Receptor; BP: Stress response

2.0 ± 0.37

2.0 ± 0.38

 hsp90aa1

Heat shock protein HSP 90-alpha

Heat Shock Response (#1)

MF: Chaperone; BP: Stress response

3.1 ± 0.31

3.7 ± 0.67

 hsp90ab1

Heat shock protein HSP 90-beta

Heat Shock Response (#1)

MF: Chaperone; BP: Stress response

1.3 ± 0.19

1.4 ± 0.22

 hspd1

60 kDa heat shock protein

Heat Shock Response (#1)

MF: Chaperone, Isomerase; BP: Stress response

0.3 ± 0.02

0.4 ± 0.04

 serpinh1 (hsp47)

Serpin H1

Heat Shock Response (#1)

MF: Chaperone; BP: Stress response, Collagen biosynthesis

5.5 ± 0.89

6.3 ± 0.78

Genes Related to Stress Response

 calm (cam)

Calmodulin

Cellular Stress (#2), Oxidative Stress (#3)

MF: Calcium ion binding; BP: Calcium-mediated signaling

0.4 ± 0.06

0.4 ± 0.04

 cat

Catalase

Cellular Stress (#2), Oxidative Stress (#3) Apoptosis (#4)

MF: Oxidoreductase, Peroxidase; BP: Hydrogen peroxide

1 ± 0.14

1 ± 0.11

 cirbp

Cold-inducible RNA-binding protein

Heat Shock Response (#1)

Cellular Stress (#2), Oxidative Stress (#3)

MF: Activator, Repressor, RNA-binding; BP: Stress response

0.4 ± 0.03

0.3 ± 0.03

 cldn3

Claudin 3

Cellular Stress (#2),

MF: Transmembrane signaling; BP: Tight junction, Protein binding

0.8 ± 0.07

1 ± 0.1

 cul3

Cullin 3

Cellular Stress (#2), Apoptosis (#4)

MF: Protein ubiquitination; BP: ER-Golgi transport, Transport

1.2 ± 0.08

1 ± 0.06

 cyp1a1

Cytochrome P450 1A1

Cellular Stress (#2), Oxidative Stress (#3)

MF: Oxidoreductase; BP: Oxidation-reduction process

0.2 ± 0.05

0.2 ± 0.04

 egln2 (phd1)

Egl nine homolog 2

Cellular Stress (#2), Oxidative Stress (#3), Apoptosis (#4)

MF: Oxidoreductase, Oxygen sensor activity; BP: Cell redox homeostasis, Response to hypoxia

0.4 ± 0.03

0.4 ± 0.05

 gstt1

Glutathione S-transferase theta-1

Cellular Stress (#2), Oxidative Stress (#3)

MF: Transferase; BP: Glutathione metabolic process

0.6 ± 0.09

0.5 ± 0.09

 hcn1

Hyperpolarization-activated cyclic nucleotide-gated channel 1

Cellular Stress (#2), Oxidative Stress (#3)

MF: Ion channel; BP: Ion transport, Transport

5.4 ± 1.27

5.7 ± 1.06

 hif1α

Hypoxia-inducible factor 1 alpha

Cellular Stress (#2), Oxidative Stress (#3), Immune (#5)

MF: DNA-binding; Oxygen sensor activity; BP: Transcription regulation, Response to hypoxia

0.60 ± 0.06

0.57 ± 0.06

 igfbp2b1

Insulin-like growth factor-binding protein 2 - paralog b1

Oxidative Stress (#3)

MF: Growth factor binding; BP: Growth regulation

0.6 ± 0.14

0.6 ± 0.15

 jak2

Tyrosine-protein kinase JAK2-like

Cellular Stress (#2), Oxidative Stress (#3), Apoptosis (#4), Immune (#5)

MF: Chromatin regulator, Tyrosine-protein kinase; BP: Apoptosis, Immunity

1.7 ± 0.22

1.5 ± 0.16

 jund

Transcription factor Jun-D-like

Cellular Stress (#2), Apoptosis (#4), Immune (#5)

MF: Activator, DNA-binding; BP: Transcription, Transcription regulation

3.2 ± 0.53

3 ± 0.35

 ndufa1

NADH dehydrogenase 1 alpha subcomplex subunit 1

Cellular Stress (#2), Oxidative Stress (#3)

MF: NADH dehydrogenase; BP: Electron transport, Respiratory chain

1 ± 0.05

1 ± 0.02

 ndufa4

Cytochrome c oxidase subunit NDUFA4

Cellular Stress (#2), Oxidative Stress (#3)

MF: NADH dehydrogenase; BP: Electron transport, Respiratory chain

2.2 ± 0.43

1.3 ± 0.45

 prdx6

Peroxiredoxin 6

Cellular Stress (#2), Oxidative Stress (#3)

MF: Antioxidant, Peroxidase; BP: Cellular response to oxidative stress

0.4 ± 0.01

0.4 ± 0.02

 rraga

Ras-related GTP-binding protein A

Cellular Stress (#2), Oxidative Stress (#3), Apoptosis (#4)

MF: GTP-binding, Hydrolase; BP: Apoptosis

0.5 ± 0.04

0.5 ± 0.03

 txn

Thioredoxin

Cellular Stress (#2), Oxidative Stress (#3) Apoptosis (#4)

MF: Activator; BP: Oxidation-reduction process

1.9 ± 0.37

1.5 ± 0.26

 ucp2

Mitochondrial uncoupling protein 2

Cellular Stress (#2), Oxidative Stress (#3), Apoptosis (#4)

MF: Oxidative phosphorylation; BP: Transport

0.2 ± 0.04

0.2 ± 0.03

Genes Related to Immune Response

 apod

Apolipoprotein D-like

Immune (#5), Apoptosis (#4), Oxidative Stress (#3)

MF: Lipid-binding, Lipid transport; BP: Transport, Immunity

4.4 ± 2.73

7.7 ± 2.55

 c1ql2

Complement C1q-like protein 2

Immune (#5), Apoptosis (#4)

MF: Protein binding; BP: Defence response to bacterium

6.4 ± 0.78

12.3 ± 4.47

 c3

Complement C3-like

Immune (#5)

MF: Signaling receptor binding; BP: Complement alternate pathway, Inflammatory response, Innate immunity

0.6 ± 0.11

0.6 ± 0.12

 camp-a

Cathelicidin - paralog a

Immune (#5)

MF: Antimicrobial peptide; BP: Bacterial defence

0.9 ± 0.2

3 ± 0.89

 casp8

Caspase 8

Immune (#5), Apoptosis (#4)

MF: Hydrolase, Protease, Thiol-protease; BP: Apoptosis, Host-virus interaction

1.7 ± 0.12

1.6 ± 0.11

 ctsh

Cathepsin H precursor

Immune (#5), Apoptosis (#4)

MF: Hydrolase, Protease, Thiol-protease;

BP: Proteolysis

0.3 ± 0.03

0.3 ± 0.03

 epx

Eosinophil peroxidase-like

Immune (#5),

Oxidative Stress (#3)

MF: Oxidoreductase, Peroxidase; BP: Bacterial defence, Oxidative stress response

3.1 ± 0.85

2.3 ± 0.57

 il8 (cxcl8)

Interleukin 8 (Chemokine CXC)

Immune (#5)

MF: Cytokine; BP: Chemotaxis, Inflammatory response

1.4 ± 0.33

2.6 ± 0.73

 irf2

Interferon regulatory factor 2

Immune (#5)

MF: Activator, DNA-binding, Repressor; BP: Transcription regulation

0.8 ± 0.15

0.8 ± 0.17

 mhcii (hla-dra)

MHC class ii antigen alpha chain

Immune (#5)

MF: Peptide antigen binding; BP: Adaptive immunity, Immunity

1 ± 0.16

1.5 ± 0.32

 mmp9

Matrix metalloproteinase 9

Immune (#5), Apoptosis (#4)

MF: Hydrolase, Metalloprotease, BP: Collagen degradation

2 ± 0.54

1.4 ± 0.25

 nckap1l

Nck-associated protein 1-like

Immune (#5), Apoptosis (#4)

MF: Protein kinase activator; BP: Apoptosis

0.6 ± 0.05

0.6 ± 0.04

 tapbp

Tapasin

Immune (#5)

MF: Peptide antigen binding; BP: Immune response, Antigen presentation

0.8 ± 0.17

0.9 ± 0.21

 tnfrsf6b

Tumor necrosis factor receptor superfamily member 6b

Immune (#5), Apoptosis (#4)

MF: Signaling Receptor; BP: Apoptosis

1.6 ± 0.45

2.8 ± 0.71

Genes Related to Cellular Metabolism

 gck

Glucokinase

Cellular Metabolic Processes (#10)

MF: Allosteric enzyme, Kinase, Transferase; BP: Glycolysis

0.5 ± 0.25

0.7 ± 0.35

 pdk3

Pyruvate dehydrogenase [lipoamide] kinase isozyme 3

Cellular Metabolic Processes (#10)

MF: Kinase, Transferase; BP: Carbohydrate metabolism, Glucose metabolism

1.8 ± 0.15

1.3 ± 0.11

Gene Related to Transcriptional Regulation

 dnmt1

DNA (cytosine-5)-methyltransferase 1

Transcription (#7)

MF: Chromatin regulator, DNA-binding, Methyltransferase; BP: DNA methylation

0.5 ± 0.02

0.5 ± 0.04

  1. a Refers to the identity of the 44 K microarray-identified genes selected for qPCR validation. Gene abbreviations are according to UniProt terminology. Further details about primer sequences and BLASTn hits for gene identification purposes are given in Additional files 10 and 11
  2. b Categories of functional themes as identified in the GO/pathway term network analysis: Heat Shock Response (#1), Cellular Stress (#2), Oxidative Stress (#3), Apoptosis (#4), Immune Response (#5), Protein Processing & Localization (#6), Transcription (#7), Proteolysis (#8), Catabolic Processes (#9) and Cellular Metabolic Processes (#10) (see Figs. 3 and 4)
  3. c Key molecular function (MF) and biological process (BP) terms according to UniProt database for each gene
  4. d Mean fold change (FC) ± S.E.M for the Warm & Normoxic (WN) group based on Fluidigm Biomark™ qPCR validation
  5. e Mean fold change (FC) ± S.E.M for the Warm & Hypoxic (WH) group based on Fluidigm Biomark™ qPCR validation