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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.