Table 3 Predicted target genes with immune response related function from in silico analysis using the Atlantic salmon transcriptome as input (holistic apporach)
Gene | Gene function1 | Predicted by four search tools2 | Predicted by three search tools3 | Reference4 |
|---|---|---|---|---|
Interferon regulatory factor 2-binding protein 2-A | Repressor, regulation of transcription, represses the NFAT1-dependent transactivation of NFAT-responsive promoters | miR-223_5p | − | NM_001139853.1 |
interferon regulatory factor 5 (IRF5) | Transcription factor activator that promote inflammation, innate immune system, Antiviral defense | miR-181c-5p | miR-462a-3p | NM_001139852.1 |
CD226 antigen precursor | Activator, Receptor involved in cytokine production, regulation of immune response in innate immune system | miR-146a-3p, miR-181c-5p | miR-7132-3p | NM_001139914.1 |
POU domain class 2-associating factor 1 | Transcriptional coactivator, humoral immune response | miR-181c-5p | − | NM_001140075.1 |
Suppressor of IKK-epsilon | inhibitory role in virus- and TLR3-triggered IRF3, Inhibits TLR3-mediated activation of interferon-stim. response elements (ISRE) | miR-146a-3-3p, miR-146a-3p | miR-21a-2-3p, miR-21b-3p | NM_001140308.1 |
NF-kappa-B inhibitor epsilon | Inhibition of NFkB, innate immune system signaling pathway | miR-181c-5p | miR-146b-5p | NM_001140380.1 |
Interferon-induced protein 44 (IFI44) | GTP binding, antiviral defense | miR-21b-3p | miR-21a-2-3p | NM_001140400.1 |
C-C chemokine receptor type 9 | Transcription coactivator binding, chemokine receptor activity, immune response | − | miR-181c-5p, miR-731-5p | NM_001140518.1 |
C-C motif chemokine 25 precursor | Effector, chemokine-mediated signaling pathway, immune response, inflammatory response | miR-155-5p | − | NM_001140865.1 |
C-X-C motif chemokine 10 precursor | Chemokine-mediated signaling pathway, effector, immune response, inflammatory response | miR-181c-5p | :miR-21b-3p | NM_001141028.1 |
Interleukin-20 receptor alpha chain precursor | Activator, cytokine-mediated signaling pathway, Interleukin 20 binding, immune system | − | miR-92a-3-5p | NM_001141080.1 |
C-C motif chemokine 21 precursor | Chemokine-mediated signaling pathway, effector, immune response, inflammatory response | miR-92a-3-5p | miR-21a-2-3p, miR-21b-3p | NM_001141267.2 |
interferon-induced, ds RNA-activated protein kinase | Activator and effector, Antiviral defense, Host-virus interaction, Immunity, Innate immunity, Transcription, Transcription regulation | miR-146b-5p | − | NM_001141332.2 |
C-C chemokine receptor type 3 | Effector, chemokine receptor activity, inflammatory response, Host-virus interaction, cellular defense response | − | miR-7132-3p | NM_001173762.1 |
Interleukin-31 receptor A precursor | Transcription coactivator, activates STAT3, cytokine receptor activity, acute inflammatory response to antigenic stimulus | − | miR-1338-3p | NM_001173970.1 |
interferon regulatory factor 1 (IRF1) isoform 2 | Activator, promote antiviral innate immunity response, Transcription regulation | miR-462b-5p | miR-7132-5p | NM_001252364.1 |
interleukin 1 receptor accessory protein precursor | Activator, IL-1 signaling pathway, Immunity, Inflammatory response, innate immune response | miR-2188-3p | − | NM_001123552.1 |
CCL4-like chemokine precursor | Effector, chemokine-mediated signaling pathway, immune response, inflammatory response | miR-146a-3-3p, miR-146a-3p | − | NM_001123618.1 |
C-C chemokine receptor type 6 | C-C chemokine binding, cellular defense response, innate immune response | miR-181c-5p | − | NM_001139972.1 |
Interferon regulatory factor 4 (IRF4) | Transcriptional activator, type I interferon signaling pathway, binds to ISRE, immune system pathways | − | miR-731-5p | NM_001139982.1 |
Interleukin-13 receptor alpha-2 chain precursor | Cytokine receptor activity, immunoglobulin mediated immune response, negative regulation of immunoglobulin production | miR-731-3p | miR-731-5p | NM_001140169.1 |
C-X-C chemokine receptor type 3 | Receptor for C-X-R chemokines, regulates biological processes such as inflammation, immunity, and would healing | miR-731-5p | miR-734-3p | NM_001140493.1 |
nuclear factor NF-kappa-B p100 subunit | Activator and repressor, transcr. factor activity, NF-kappaB signaling pathway, innate immune response, innflammatory response | − | miR-462a-3p | NM_001173583.1 |
toll-like leucine-rich repeat precursor | Activator, Immunity, Inflammatory response, Innate immunity | miR-731-5p | miR-2188-3p | NM_001123691.1 |
Macrophage migration inhibitory factor (MIF) | Inhibitor/surpressor, Inflammatory response, innate immune response, cell-mediated immunity | miR-155-5p | − | NM_001141547.1 |
BCL2/adenovirus E1B interacting protein 3-like | Effector, negative regulation of apoptotic process, Host-virus interaction, defense response to virus | miR-1338-3p, miR-146b-5p, miR-181c-5p, miR-731-5p | − | NM_001141679.1 |
TRAF2-binding protein | mediates the IRAK1 and TRAF6 interaction following IL-1 stimulation, I-kappaB kinase/NF-kappaB signaling | − | miR-462a-3p | NM_001173784.1 |
single Ig IL-1-related receptor precursor | Acute-phase response, neg. reg. of cytokine-mediated signaling pathway, neg. reg.of sequence-specific DNA binding transcription factor activity | miR-181c-5p, miR-462a-3p | − | NM_001173838.1 |