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Table 3 Predicted target genes with immune response related function from in silico analysis using the Atlantic salmon transcriptome as input (holistic apporach)

From: Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection

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
  1. 1Key words about gene function are based on gene function description in the http://www.uniprot.org/uniprot/ database. 2DE-miRs predicted to target the gene by all the four target search tools used (RNA-hybrid, TargetSpy, PITA, Miranda)
  2. 3DE-miRs predicted to target the gene by three of the four target search tools used. 4Genbank reference number