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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