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. 2012 Aug 28;13:431. doi: 10.1186/1471-2164-13-431

Table 2.

Selected probes1 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

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 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
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 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
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 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
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

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 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.

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.