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Table 1 Selected probes 1 representing immune-relevant genes that were differentially expressed between fish injected with PBS or pIC and sampled at 6 hours post-injection (6HPI) at 10 or 16°C, or between fish injected with pIC but held at 10 vs. 16°C and sampled at 6HPI

From: A moderate increase in ambient temperature modulates the Atlantic cod (Gadus morhua) spleen transcriptome response to intraperitoneal viral mimic injection

Probes identified as differentially expressed (FDR = 1%) between PBS 6HPI@ 10°C and pIC 6HPI@ 10°C, and between PBS 6HPI@ 16°C and pIC 6HPI@ 16°C2

Probe ID

Best BLASTx hit3

Fold-change (pIC @ 16°C / PBS @ 16°C)4

Fold-change (pIC @ 10°C / PBS @ 10°C)4

Fold-change (pIC @ 16°C / pIC @ 10°C)4

38613

Interferon stimulated gene 15 [Gadus morhua]

55.97

5.29

8.45

38285

DExD/H box RNA helicase [Paralichthys olivaceus] (Aliases: DHX58, LGP2)

5.13

2.44

2.41

45882

Retinoic acid receptor responder protein 3 [Osmerus mordax] (Alias: HRAS-suppressor like 3)

12.17

5.51

-

38260

Phosphoinositide phospholipase C-eta-2 [Homo sapiens]

5.08

2.19

2.28

44546

Interferon regulatory factor 1 (IRF1) [Gadus mohua]

4.74

1.88

2.48

36426

Cell division cycle 42 [Sus scrofa]

4.00

2.16

1.85

38042

Deoxyribonuclease gamma precursor [Oncorhynchus mykiss]

3.41

1.45

2.18

41397

Prostaglandin E synthase 3 [Osmerus mordax]

2.86

1.87

-

44530

NF-kappa-B inhibitor alpha (IκBα) [Gadus morhua]

2.15

3.12

-

40721

Nostrin protein [Danio rerio]

2.12

2.04

-

39371

Novel immune-type receptor 4 [Oncorhynchus mykiss]

2.03

1.52

-

41181

Ubiquitin carboxyl-terminal hydrolase 5 [Salmo salar]

1.88

2.04

-

36482

CXC chemokine [Psetta maxima]

1.74

1.71

-

Probes identified as differentially expressed (FDR = 1%) between PBS 6HPI@10°C and pIC 6HPI@10°C only 2

Probe ID

Best BLASTx hit 3

Fold-change (pIC @ 16°C / PBS @ 16°C) 4

Fold-change (pIC @ 10°C / PBS @ 10°C) 4

Fold-change (pIC @ 16°C / pIC @ 10°C) 4

46031

Synaptic vesicle glycoprotein 2B [Harpegnathos saltator]

-

3.35

-

44581

NF-kappa-B inhibitor alpha (IκBα) [Gadus morhua]

-

1.46

-

37564

Heat shock protein 90 alpha [Paralichthys olivaceus]

-

-1.50

-

49256

Unknown

-

-10.59

-

Probes identified as differentially expressed (FDR = 1%) between PBS 6HPI@16°C and pIC 6HPI@16°C only 2

Probe ID

Best BLASTx hit 3

Fold-change (pIC @ 16°C / PBS @ 16°C) 4

Fold-change (pIC @ 10°C / PBS @ 10°C) 4

Fold-change (pIC @ 16°C / pIC @ 10°C) 4

44448

Small inducible cytokine SCYA104 [Paralabidochromis chilotes] (Alias: gmSCYA123a)

24.34

-

7.29

38356

Sacsin [Homo sapiens] (Alias: SACS)

12.54

-

11.14

48390

Endonuclease domain-containing 1 protein precursor [Salmo salar]

9.94

-

-

39328

Zinc finger, NFX1-type containing 1 (ZNFX1) [Homo sapiens]

9.05

-

2.67

43196

VHSV-induced protein [Oncorhynchus mykiss]

8.03

-

3.35

38639

Interleukin-8 variant 5 (IL-8) [Ictalurus punctatus]

7.60

-

5.88

43201

Viperin [Niphon spinosus] (Aliases: Radical S-adenosyl methionine domain containing protein 2, RSAD2)

6.89

-

5.43

50762

Unknown

6.70

-

-

37299

GADD45 alpha [Anoplopoma fimbria]

2.27

-

3.19

38617

Interferon-inducible GTPase a [Salmo salar]

6.53

-

2.80

47384

Unnamed protein product [Tetraodon nigroviridis]

6.50

-

7.71

36121

Anti-apoptotic protein NR-13 [Gadus morhua]

4.44

-

-

37609

Hepcidin precursor [Gadus morhua]

4.30

-

-

36384

CC chemokine type 3 [Gadus morhua]

3.55

-

-

44371

Probable E3 ubiquitin-protein ligase RNF144A-A [Esox lucius]

3.43

-

-

36190

Bloodthirsty [Gadus morhua]

3.38

-

2.05

37904

Type 2 double stranded RNA activated protein kinase [Gadus morhua] (Alias: PKR)

2.98

-

2.52

44579

Mitogen-activated protein kinase kinase 4 [Gadus morhua]

2.76

-

1.90

38599

Interferon regulatory factor 10 (IRF10) [Paralichthys olivaceus]

2.63

-

-

38655

Interferon regulatory factor 7 (IRF7) [Psetta maxima]

2.49

-

2.15

38788

Mannose-specific lectin precursor [Esox lucius]

2.39

-

-

39119

Ras homolog gene family, member T1a [Danio rerio]

2.25

-

1.75

38625

Interleukin 12 receptor beta 2.b [Danio rerio]

2.12

-

-

36407

CD9 antigen [Salmo salar]

2.05

-

1.44

44615

Toll-like receptor 9 (TLR9) [Gadus morhua]

2.03

-

-

37854

Interferon-inducible protein Gig2 [Siniperca chuatsi]

2.01

-

-

35877

Alpha-2-macroglobulin [Epinephelus coioides]

1.94

-

-

41703

Ras-related protein Rab-10 [Salmo salar]

1.90

-

-

36380

CC chemokine type 2 [Gadus morhua]

1.89

-

-

36142

Beta-2-microglobulin [Gadus morhua]

1.73

-

-

38629

Interleukin-1 receptor-associated kinase 4 (IRAK4) [Gadus morhua]

1.67

-

-

38090

GTPase IMAP family member 7 [Salmo salar]

1.64

-

-

36328

FLICE-like inhibitory protein [Oryzias latipes]

1.58

-

1.40

45132

DEAD (Asp-Glu-Ala-Asp) box polypeptide 10-like [Bos taurus]

1.55

-

-

44434

Type 1 death domain-containing protein [Gadus morhua]

1.48

-

-

41613

Dhx33 protein [Xenopus laevis]

1.47

-

-

37498

GTP-binding nuclear protein Ran [Osmerus mordax]

1.43

-

1.36

36122

Novel protein similar to BCL2-related ovarian killer [Danio rerio]

1.43

-

-

44431

Caspase 10 [Gadus morhua]

1.33

-

1.34

37561

Stress-70 protein, mitochondrial precursor [Salmo salar] (Alias: Mortalin)

1.32

-

-

44606

Toll-like receptor 3 (TLR3) [Gadus morhua]

1.32

-

-

  1. 1Probes presented in this table were selected based on their known roles in vertebrate immune responses. Some genes without a BLASTx hit (e.g. Unknowns) were added because they presented a pIC-induced fold-change higher than 5, and therefore, could represent novel immune-relevant genes. For a complete list of microarray-identified informative probes please refer to Additional file1: Tables S2-S5 and S7-S8.
  2. 2Fold-change in probe expression is also shown for pIC @ 16°C vs. pIC @ 10°C when significant differential expression was found in the PBS vs. pIC comparisons.
  3. 3Informative genes were re-annotated using the contig or EST from which the probe printed in the array was designed by comparing the referred sequence to the NCBI’s nr database using the BLASTx algorithm as implemented by Blast2GO[67]. The best BLASTx hit (E-value cutoff of 10-5) with an informative name (i.e. not predicted, probable or unnamed protein) is presented in this table. Synonyms were obtained from SWISS-PROT, GENE CARDS and other BLASTx hits as long as they had E-value < 10-5, or from the literature (aBorza et al.[58]).
  4. 4Fold-changes are only reported when probes were differently expressed (FDR = 1%) in a given comparison (e.g. pIC@10°C vs. pIC@16°C) and are shown as outputted by siggenes; otherwise a dash (−) is presented in place of the fold-change. Fold-change values preceded by a minus (“-“) sign represent overall fold down-regulation for a particular comparison. For standard deviation, p- and d-values, please refer to Additional file1: Tables S2-S5 and S7-S8.
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BMC Genomics

ISSN: 1471-2164

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