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Table 2 Reverse regulatory association of 3 differentially expressed miRNAs and their 37 predicted target genes in HCV replicon clones vs. Huh-7

From: An integrated approach identifies IFN-regulated microRNAs and targeted mRNAs modulated by different HCV replicon clones

 

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

HNMTâ–²

histamine N-methyltransferase

227509

1.423

0.039

unclassified|IRGâ–²

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

XPO1â–²

exportin 1 (CRM1 homolog, yeast)

105030

0.748

0.002

Intracellular protein transport|IRGâ–²

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

PMPCBâ–²

peptidase (mitochondrial processing) beta

210046

0.684

0.015

Oxidoreductase activity|IRGâ–²

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

HMGB1â–²

high-mobility group box 1

151074

0.586

0.011

Proinflammatory cytokine|IRGâ–²

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

  1. § Gene targeted by two down-regulated miRs
  2. â–² Interferon regulated gene (IRG) according to the INTERFEROME database
  3. # Gene showing same direction of regulation (up or down) in microarray analysis of HCV genotype 2a chimeric virus J6/JFH infection
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BMC Genomics

ISSN: 1471-2164

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