Table 2.
Reverse regulatory association of 3 differentially expressed miRNAs and their 37 predicted target genes in HCV replicon clones vs. Huh-7
| Gene_Symbol | Gene_name | ProbeID | Fold-change | p-value | Biological process and Molecular function | |
|---|---|---|---|---|---|---|
| Down-regulated miR | ||||||
| miR-128a | CAMTA1 | calmodulin binding transcription activator 1 | 164871 | 1.426 | 0.045 | Signal transduction/Calcium mediated signaling |
| miR-128a | CAST | calpastatin | 222724 | 1.788 | 0.002 | Cysteine protease inhibitor|Select regulatory molecule |
| miR-128a | CORO1C | coronin, actin binding protein, 1C | 107201 | 1.402 | 0.027 | Cytoskeletal protein|Actin binding cytoskeletal protein |
| miR-128a | PARK7 | Parkinson disease (autosomal recessive, early onset) 7 | 136848 | 1.529 | 0.003 | Nucleic acid binding |
| miR-128a | REPS1 | RALBP1 associated Eps domain containing 1 | 147893 | 1.352 | 0.002 | Intracellular protein traffic/Endocytosis |
| miR-128a | RND3# | Rho family GTPase 3 | 129829 | 2.161 | 0.041 | G-protein|Small GTPase|Select regulatory molecule |
| miR-128a | SAA4 | serum amyloid A4, constitutive | 214434 | 1.880 | 0.029 | Apolipoprotein;Defense/immunity protein |
| miR-128a | TMCC1 | transmembrane and coiled-coil domain family 1 | 112169 | 1.369 | 0.031 | unclassified |
| miR-128a | TRAPPC4 | trafficking protein particle complex 4 | 205369 | 1.502 | 0.012 | Membrane traffic protein |
| miR-128a | UBE2E3 | ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast) | 201108 | 1.505 | 0.030 | Ligase|Other ligase |
| miR-128a | VAMP8 | vesicle-associated membrane protein 8 (endobrevin) | 226943 | 2.586 | 0.011 | SNARE protein|Membrane traffic protein |
| miR-196a | ARMET | arginine-rich, mutated in early stage tumors | 144765 | 1.816 | 0.029 | unclassified |
| miR-196a | HADH2 | hydroxyacyl-Coenzyme A dehydrogenase, type II | 142475 | 1.421 | 0.031 | Oxidoreductase|Reductase|Dehydrogenase;Oxidoreductase |
| miR-196a | HIST1H2BD | histone 1, H2bd | 148940 | 2.656 | 0.020 | DNA binding |
| miR-196a | HNMT▲ | histamine N-methyltransferase | 227509 | 1.423 | 0.039 | unclassified|IRG▲ |
| miR-196a | LAMA4 | laminin, alpha 4 | 101059 | 2.660 | 0.033 | Extracellular matrix|Extracellular matrix linker protein |
| miR-196a | LTB4DH# | leukotriene B4 12-hydroxydehydrogenase | 210882 | 1.961 | 0.001 | Oxidoreductase|Reductase|Dehydrogenase;Oxidoreductase |
| miR-196a | PI3 | peptidase inhibitor 3, skin-derived (SKALP) | 128827 | 2.558 | 0.018 | Proteolysis|Protein metabolism and modification |
| miR-196a | RIOK3# | RIO kinase 3 (yeast) | 142169 | 3.226 | 0.018 | Protein metabolism and modification|Protein phosphorylation |
| miR-196a | RRAGA | Ras-related GTP binding A | 105497 | 1.243 | 0.023 | G-protein|Small GTPase|Select regulatory molecule |
| miR-196a | ZMYND11 | zinc finger, MYND domain containing 11 | 161540 | 1.665 | 0.036 | Transcription factor|Transcription cofactor |
| miR-128a/miR-196a | CENPE§ | centromere protein E, 312kDa | 165425 | 1.436 | 0.018 | Structural constituent of cytoskeleton |
| Up-regulated miR | ||||||
| miR-142-3p | ZCCHC14 | zinc finger, CCHC domain containing 14 | 200292 | 0.759 | 0.035 | unclassified |
| miR-142-3p | XPO1▲ | exportin 1 (CRM1 homolog, yeast) | 105030 | 0.748 | 0.002 | Intracellular protein transport|IRG▲ |
| miR-142-3p | ATAD2 | ATPase family, AAA domain containing 2 | 114584 | 0.745 | 0.007 | Hydrolase activity |
| miR-142-3p | TRIM33 | tripartite motif-containing 33 | 134526 | 0.714 | 0.004 | Transcription cofactor;Nucleic acid binding|Transcription factor |
| miR-142-3p | RAB1A | RAB1A, member RAS oncogene family | 122650 | 0.704 | 0.045 | G-protein|Small GTPase|Select regulatory molecule |
| miR-142-3p | TFG | TRK-fused gene | 210281 | 0.686 | 0.026 | unclassified |
| miR-142-3p | PMPCB▲ | peptidase (mitochondrial processing) beta | 210046 | 0.684 | 0.015 | Oxidoreductase activity|IRG▲ |
| miR-142-3p | ZNF226 | zinc finger protein 226 | 178824 | 0.682 | 0.043 | Zinc finger transcription factor |
| miR-142-3p | ANKHD1 | ankyrin repeat and KH domain containing 1 | 224628 | 0.658 | 0.006 | unclassified |
| miR-142-3p | CXADR | coxsackie virus and adenovirus receptor | 108284 | 0.620 | 0.025 | Other receptor|Receptor |
| miR-142-3p | CHAF1B# | chromatin assembly factor 1, subunit B (p60) | 174351 | 0.586 | 0.017 | Nucleic acid binding|Chromatin/chromatin-binding protein |
| miR-142-3p | HMGB1▲ | high-mobility group box 1 | 151074 | 0.586 | 0.011 | Proinflammatory cytokine|IRG▲ |
| miR-142-3p | BNIP3 | BCL2/adenovirus E1B 19kDa interacting protein 3 | 109165 | 0.551 | 0.000 | unclassified |
| miR-142-3p | COG4 | component of oligomeric golgi complex 4 | 151150 | 0.394 | 0.042 | Other RNA-binding protein|Nucleic acid binding |
| miR-142-3p | USH1C | Usher syndrome 1C (autosomal recessive, severe) | 195953 | 0.367 | 0.016 | Cytoskeletal protein |
§ Gene targeted by two down-regulated miRs
▲ Interferon regulated gene (IRG) according to the INTERFEROME database
# Gene showing same direction of regulation (up or down) in microarray analysis of HCV genotype 2a chimeric virus J6/JFH infection