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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.