Table 1.
Selected probes1 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
|
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 only2 | ||||
|
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 |
| 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 only2 | ||||
|
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 |
| 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 | - | - |
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 file 1: Tables S2-S5 and S7-S8.
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.
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]).
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 file 1: Tables S2-S5 and S7-S8.