Skip to main content

Table 2 Selected probes 1 representing immune-relevant genes that were differentially expressed between fish injected with PBS or pIC at 24 hour post-injection (24HPI) at 10 or 16°C, or between fish injected with pIC but held at 10 vs. 16°C and sampled at 24HPI

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 24HPI@10°C and pIC 24HPI@10°C, and PBS 24HPI@16°C and pIC 24HPI@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

38604

Interferon stimulated gene 15 (ISG15) [Gadus morhua]

38.35

90.24

-3.05

45882

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

31.10

27.01

-

44590

RIG-I C-terminal domain-containing protein 1 [Gadus morhua] (Aliases: DHX58, LGP2)

12.13

30.48

-

48390

Endonuclease domain-containing 1 protein precursor [Salmo salar]

11.53

14.24

-

38356

Sacsin [Homo sapiens] (Alias: SACS)

9.88

17.37

-

44448

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

7.28

66.64

-2.34

38638

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

6.92

25.33

-5.66

35718

A disintegrin and metalloproteinase domain 8a [Danio rerio]

6.12

3.02

-

47329

Unnamed protein product [Tetraodon nigroviridis]

5.81

5.52

-

41269

Regulator of nonsense transcripts 1-like [Bos taurus]

5.07

13.93

-2.16

44859

Novel protein [Danio rerio]

4.98

11.50

-2.34

37854

Interferon-inducible protein Gig2 [Siniperca chuatsi]

3.41

4.14

-

44324

Aminopeptidase N [Camponotus floridanus]

3.04

3.45

-

44472

CC chemokine type 3 [Gadus morhua]

2.75

1.75

-

55231

Unknown

2.65

5.17

-

47410

Probable E3 ubiquitin-protein ligase RNF144A-A [Salmo salar]

2.64

7.10

-2.83

47613

Unnamed protein product [Tetraodon nigroviridis]

2.48

5.22

-2.72

37542

10 kDa heat shock protein, mitochondrial [Esox lucius]

2.45

1.61

-

44919

Novel protein similar to vertebrate IGSF3 [Danio rerio]

2.43

3.12

-

44371

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

2.35

4.56

-1.92

37299

GADD45 alpha [Anoplopoma fimbria]

2.25

4.52

-

44598

STAT1 [Gadus morhua]

2.12

1.98

-

36190

Bloodthirsty [Gadus morhua]

2.11

3.43

-1.78

36612

Complement component C3 [Paralichthys olivaceus]

2.07

2.47

-

43196

VHSV-induced protein [Oncorhynchus mykiss]

2.02

4.04

-

44546

Interferon regulatory factor 1 (IRF1) [Gadus mohua]

1.86

3.35

-1.84

37566

Heat shock protein HSP 90-alpha [Salmo salar]

1.80

1.34

1.55

36407

CD9 antigen [Salmo salar]

1.78

1.93

-

36426

Cell division cycle 42 [Sus scrofa]

1.66

1.93

-

35957

Apolipoprotein A-IV precursor [Salmo salar]

1.60

2.58

-1.53

38545

IgD heavy chain constant region variant b [Gadus morhua]

1.60

1.43

-

44865

Hect domain and RLD 5 [Bos Taurus]

1.52

1.94

-1.40

36923

DnaJ-like subfamily A member 4 [Paralichthys olivaceus]

1.51

1.43

-

Probes identified as differentially expressed (FDR = 1%) between PBS 24HPI@10°C and pIC 24HPI@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

38617

Interferon-inducible GTPase a [Salmo salar]

-

8.88

-

49247

Unknown

-

5.74

-2.86

43201

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

-

4.68

-2.45

38260

Phospholipase C-eta-2 [Homo sapiens]

-

4.11

-

39368

Novel immune type receptor protein [Danio rerio]

-

3.23

 

40397

Deltex-3-like [Salmo salar]

-

2.76

-2.18

39119

Ras homolog gene family, member T1a [Danio rerio]

-

2.66

-

44579

Mitogen-activated protein kinase kinase 4 [Gadus morhua]

-

2.61

-1.66

40174

60 kDa heat shock protein, mitochondrial precursor [Salmo salar]

-

2.46

-

37609

Hepcidin precursor [Gadus morhua]

-

2.44

-

36339

Caspase-1 [Dicentrarchus labrax]

-

2.42

-1.78

38788

Mannose-specific lectin precursor [Esox lucius]

-

2.30

-1.80

36364

Cathepsin L precursor [Anoplopoma fimbria]

-

2.11

-

38599

Interferon regulatory factor 10 (IRF10) [Paralichthys olivaceus]

 

2.05

-

44503

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

-

1.93

-

45146

DNA (cytosine-5-)-methyltransferase 7 [Danio rerio]

 

1.89

-1.79

44434

Type 1 death domain-containing protein [Gadus morhua]

-

1.89

-

36797

Cytotoxic and regulatory T cell protein [Oncorhynchus mykiss]

-

1.87

-1.81

40721

Nostrin protein [Danio rerio]

-

1.86

-

44839

Disulfide-isomerase A3 precursor [Salmo salar]

-

1.79

-

44518

Fas [Gadus morhua]

-

1.74

-1.77

36121

Anti-apoptotic protein NR-13 [Gadus morhua]

-

1.67

-

37498

GTP-binding nuclear protein Ran [Osmerus mordax]

-

1.64

-1.54

44550

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

-

1.63

-1.37

36328

FLICE-like inhibitory protein [Oryzias latipes]

-

1.59

-

38619

Interferon-inducible protein Gig1 [Psetta maxima]

-

1.55

-

44615

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

-

1.54

-

42836

Tumor necrosis factor receptor-2 [Paralichthys olivaceus]

-

1.54

-

42266

Strawberry notch homologue 1 [Danio rerio]

-

1.53

-

35877

Alpha-2-macroglobulin [Epinephelus coioides]

-

1.52

-

42501

T-complex protein 1 subunit delta [Takifugu rubripes]

-

1.46

-

41397

Prostaglandin E synthase 3 [Osmerus mordax]

-

1.45

-1.49

36967

E3 SUMO-protein ligase RanBP2 [Homo sapiens]

-

1.42

-

38108

Inhibitor of nuclear factor kappa-B kinase subunit alpha [Danio rerio] (Alias: IKKα)

-

1.41

-

38631

Interleukin-11a [Takifugu rubripes]

-

1.40

-

40138

78 kDa glucose-regulated protein precursor [Salmo salar]

-

1.39

-

37118

Novel protein similar to vertebrate EIF4E [Danio rerio]

-

1.35

1.31

41690

RAS guanyl-releasing protein 1 [Xenopus tropicalis]

-

1.33

-

37568

Glucose-regulated protein 94 [Paralichthys olivaceus]

-

1.33

-

39371

Novel immune-type receptor 4 [Oncorhynchus mykiss]

-

1.31

-1.33

39063

MHC class Ia antigen [Gadus morhua]

-

1.28

-

41711

Rab8b protein [Xenopus tropicalis]

-

1.27

-

35876

Alpha-2-macroglobulin receptor-associated protein [Homo sapiens]

-

1.26

-

41613

Dhx33 protein [Xenopus laevis]

-

1.24

-

45113

Methyltransferase-like protein 2 [Salmo salar]

-

-1.48

1.44

38713

KH domain-containing, RNA-binding, signal transduction-associated protein 1 [Salmo salar]

-

-1.54

-

41688

Novel protein similar to vertebrate IQGAP2 [Danio rerio]

-

-1.65

-

37695

G1/S-specific cyclin-D1 [Salmo salar]

-

-1.68

-

35934

Annexin max3 [Oryzias latipes]

-

-1.83

-

38596

Interferon induced protein 2 [Ictalurus punctatus]

-

-2.38

-

Probes identified as differentially expressed (FDR 1%) between pIC 24HPI@16°C and PBS 24HPI@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

44465

CC chemokine type 2 [Gadus morhua]

3.76

-

-

37456

Goose-type lysozyme 2 [Gadus morhua]

3.36

-

-

36381

CC chemokine type 2 [Gadus morhua]

2.98

-

-

42545

Thioredoxin [Oncorhynchus mykiss]

2.35

-

2.17

36388

CEBPA protein [Bos taurus]

1.86

-

-

36468

CCT epsilon subunit [Carassius auratus] (Alias: CCT5)

1.66

-

1.49

38014

Ctssa protein [Danio rerio]

1.66

-

-

35923

Annexin A4 [Ctenopharyngodon idella]

1.62

-

-

42502

Tcp1 protein [Danio rerio] (Alias: CCT1)

1.56

-

-

36813

DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 [Xenopus tropicalis]

1.55

-

-

40508

Glutathione S-transferase Mu 3 [Anoplopoma fimbria]

1.53

-

1.61

45010

Heat shock protein 90 alpha [Paralichthys olivaceus]

1.52

-

1.66

37573

Heat shock protein 90 alpha [Paralichthys olivaceus]

1.42

-

1.65

43222

Warm temperature acclimation protein 65–1 [Dicentrarchus labrax]

1.42

-

-

37574

Heat shock protein 90 beta [Paralichthys olivaceus]

1.37

-

1.52

39904

Peptidylprolyl isomerase A (cyclophilin A) [Danio rerio]

1.33

-

-

Probes identified as differentially expressed (FDR = 1%) between pIC 24HPI @10°C and pIC 24HPI @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

37555

Heat shock protein 47 [Oncorhynchus mykiss]

-

-

1.77

40546

Heat shock protein HSP 90-alpha [Harpegnathos saltator]

-

-

1.64

36470

Chaperonin containing TCP1 subunit 6A [Paralichthys olivaceus] (Alias: CCT6)

-

-

1.54

44902

HSP90 multi-domain protein (pfam 00183)

-

-

1.47

37544

Heat shock cognate protein 70 [Pelodiscus sinensis] (Alias: HSC71)

-

-

1.35

42467

TANK-binding kinase 1 [Gadus morhua]

-

-

-1.37

37203

Ferritin heavy subunit [Epinephelus awoara]

-

-

-1.47

41479

Protein kinase C, delta [Danio rerio]

-

-

-1.47

  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 other BLASTx hits as long as they had E-value < 10-5, or from the literature (aBorza et al.[58]). 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.
  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.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us