Table 4 Down-regulated genes in cirrhotic and non-cirrhotic HCV liver biopsy samples

Apoptosis

BCL2L12

Bcl-2-related proline-rich protein

NM_001040668.1

0.000335

Apoptosis

PDCD1

Programmed cell death protein 1 precursor

NM_005018.1

7.94E-06

carbohydrate metabolism

OGDHL

oxoglutarate dehydrogenase-like

NM_018245.1

0.000909

cell adhesion

THUMPD1

THUMP domain-containing protein 1

NM_017736.3

0.044141

Cell Cycle

AKAP4

A-kinase anchor protein 11

NM_016248.2

0.000598

cell cycle

TINF2

TERF1-interacting nuclear factor 2

NM_012461

0.045359

cell cycle

VEGFB

vascular endothelial growth factor B

NM_003377

0.017886

cell singling

GRIN3A

Glutamate [NMDA] receptor subunit 3A precursor

NM_133445.1

1.17E-06

cell singling

Q8N9G6

similar to nuclear pore membrane protein 121

XM_498333.2

7.46E-05

Cell Structure

ENO3

Beta-enolase

NM_001976.2

0.050309

cell structure

MAP6D1

MAP6 domain-containing protein 1

NM_024871.1

0.034981

cytokine

IL13RA2

Interleukin-13 receptor alpha-2 chain precursor

NM_000640.2

0.024814

Cytoskeleton

LLGL1

Lethal(2) giant larvae protein homolog 1

NM_004140.3

0.008177

cytoskeleton

SNX17

Sorting nexin-17

NM_014748.2

5.41E-05

DNA binding proteins

ZNF236

Zinc finger protein 236

NM_007345.2

1.54E-07

DNA binding proteins

ZBED4

Zinc finger BED domain-containing protein 4

NM_014838.1

0.003728

DNA replication

WRB

Tryptophan-rich protein

NM_004627.2

0.000578

Energy

ABHD2

ATP-binding cassette sub-family F member 2

NM_005692.3

0.000193

Energy

ATAD2

ATPase family AAA domain-containing protein 2

NM_014109.2

8.59E-06

Energy

PSMD11

26S proteasome non-ATPase regulatory subunit 11

NM_002815.2

0.000415

Energy

PSMD4

26S proteasome non-ATPase regulatory subunit 4

NM_002810.2

0.003878

Energy

SYDE1

synapse defective 1

NM_033025.4

0.000222

Immune response

ATG16L2

ATG16 autophagy related 16-like 2

NM_033388.1

1.31E-05

Immune response

IL8RB

High affinity interleukin-8 receptor B

NM_001557.2

0.00539

immune response

PTGS2

prostaglandin-endoperoxide synthase 2

NM_000963

0.00504

immune response

FAM14B

Interferon alpha-inducible protein 27-like protein 1

NM_145249

0.006008

immune response

OAS2

2'-5'-oligoadenylate synthase 2

NM_016817

0.009299

Ion transport

DSG4

Desmoglein-4 precursor

NM_177986.2

1.23E-05

Ion transport

SLC10A5

Sodium/bile acid cotransporter 5 precursor

NM_001010893.2

6.5E-08

Ion transport

CAPN7

Calpain-7

NM_014296.2

0.003785

ion transport

MT1E

Metallothionein-1E

NM_175617.3

0.001767

Lipid Metabolism

DEGS2

sphingolipid C4-hydroxylase/delta 4-desaturase

NM_206918.1

0.008105

lipid metabolism

CHKA

Choline kinase alpha

NM_001277.2

0.003609

lipid metabolism

ADA

bubblegum related protein

NM_030924.3

6.6E-05

Metabolism

HMGCL

Hydroxymethylglutaryl-CoA lyase, mitochondrial precursor

NM_000191.2

0.010122

metabolism

HMGCS1

Hydroxymethylglutaryl-CoA synthase, cytoplasmic

NM_002130.4

1.2E-05

Metabolism

SH3BGRL3

SH3 domain-binding glutamic acid-rich-like protein 3

NM_031286.3

0.000157

Metabolism

ARHGAP5

Rho GTPase-activating protein 5

NM_001173.2

0.010513

Metabolism

CKM

Creatine kinase M-type

NM_001824.2

0.000689

Metabolism

CPT1A

Carnitine O-palmitoyltransferase I, liver isoform

NM_001031847.1

0.008256

Metabolism

USP53

Inactive ubiquitin carboxyl-terminal hydrolase 53

NM_019050.1

2.46E-06

morphogenesis

SLC33A1

Acetyl-coenzyme A transporter 1

NM_004733.2

8.12E-06

morphogenesis

PDYN

Beta-neoendorphin-dynorphin precursor

NM_024411.2

0.055803

nervous system

NINJ2

Ninjurin-2 (Nerve injury-induced protein 2)

NM_016533.4

0.004163

protein Metabolism

GON4L

GON-4-like protein

NM_001037533.1

0.00137

protein Metabolism

PHACTR4

phosphatase and actin regulator 4 isoform 1

NM_001048183.1

0.000139

protein Metabolism

OTUD7A

OTU domain-containing protein 7A

XM_001127986.1

0.00394

protein Metabolism

Q96NT9

GR AF-1 specific protein phosphatase

XM_497354.1

7.5E-05

protein Metabolism

WFDC13

Protein WFDC13 precursor

NM_172005.1

0.080737

Protein modulation

SMAP1

Stromal membrane-associated protein 1

NM_001044305.1

8.97E-08

Protein modulation

DYRK1B

Dual specificity tyrosine-phosphorylation-regulated kinase 1B

NM_004714.1

0.001009

Protein modulation

COQ5

Ubiquinone biosynthesis methyltransferase COQ5

NM_032314.3

2.07E-05

Protein modulation

MTIF2

Translation initiation factor IF-2

NM_001005369.1

0.002917

Protein synthesis

MRPL46

39S ribosomal protein L46, mitochondrial precursor

NM_022163.2

2.83E-06

Protein synthesis

MRPS35

28S ribosomal protein S35, mitochondrial precursor

NM_021821.2

0.000245

protein synthesis

PLAT

Tissue-type plasminogen activator precursor

NM_000930.2

0.014382

protein synthesis

SENP1

Sentrin-specific protease 1

NM_014554.2

1.63E-06

protein synthesis

ELL

RNA polymerase II elongation factor ELL

NM_006532.2

0.003242

Protein synthesis

PACS1

Phosphofurin acidic cluster sorting protein 1

NM_018026.2

0.005118

protein synthesis

PTP4A1

Protein tyrosine phosphatase type IVA protein 1

NM_003463.3

0.001949

PTMs

SNF1LK

Serine/threonine-protein kinase SNF1-like kinase 1

NM_173354.3

0.000169

Reproduction

LOC283116

similar to Tripartite motif protein 49

XR_016154.1

5.32E-07

Reproduction

Q5VYG3

OTTHUMP00000018545

-

2.51E-05

RNA modelling and synthesis

EXOSC2

Exosome complex exonuclease RRP4

NM_014285.4

0.080373

RNA modelling and synthesis

RBM41

RNA-binding protein 41

NM_018301.2

0.002623

RNA modelling and synthesis

ADCY2

Double-stranded RNA-specific adenosine deaminase

NM_001111.3

6.64E-05

Signal Transduction

FGF17

Fibroblast growth factor 17 precursor

NM_003867.2

0.000254

Signal Transduction

ADH1A

Adenylate cyclase type 2

NM_020546.2

0.00139

Signal Transduction

HOMER1

Homer protein homolog 1

NM_004272.3

0.011954

Signal Transduction

TMEM100

Transmembrane protein 100

NM_018286.1

3.31E-05

sulphur metabolism

FAM62B

family with sequence similarity 62

NM_020728.1

1.6E-05

transcriptional regulation

CRAMP1L

Protein cramped-like

NM_020825.2

0.006587

transcriptional regulation

FOXK2

Forkhead box protein K2

XM_001134364.1

0.00156

transcriptional regulation

HMGN2

Nonhistone chromosomal protein HMG-17

XM_001133530.1

0.01162

Transcriptional regulation

NANOGP8

Homeobox protein NANOGP8

-

0.000264

transcriptional regulation

NFXL1

nuclear transcription factor

NM_152995.4

8.53E-05

transcriptional regulation

NR1I3

Orphan nuclear receptor NR1I3

NM_001077470.1

0.00247

Transcriptional regulation

SNORA32

Protein JOSD3

NR_003032.1

0.107321

Transcriptional regulation

GTF2B

Transcription initiation factor IIB

NM_001514.3

0.002357

Transcriptional regulation

PAX8

Paired box protein Pax-8

NM_003466.3

4.89E-05

Transcriptional regulation

CTCFL

Transcriptional repressor CTCFL

NM_080618.2

0.003129

Transcriptional regulation

EEF1AL3

Eukaryotic translation elongation factor 1 alpha 1

-

0.000917

Transcriptional regulation

INTU

PDZ domain-containing protein 6

NM_015693.2

0.003842

transcriptional regulation

TGFBR2

TGF-beta receptor type-2 precursor

NM_001024847.1

0.007651

Transport

KIF1A

Kinesin-like protein KIF1A

NM_004321.4

0.002119

transport

NUP160

Nuclear pore complex protein Nup160

NM_015231.1

3.11E-06

transport

SLIT3

Slit homolog 3 protein precursor

NM_003062.1

0.000577

Transport

AMICA1

Junctional adhesion molecule-like precursor

NM_153206.1

3.86E-06

Transport

KIF17

Kinesin-like protein KIF17

NM_020816.1

0.007279

Transport

SCAMP4

secretory carrier membrane protein 4

NM_079834.2

0.026864

transport

MUC6

Mucin-6 precursor (Gastric mucin-6)

XM_290540.7

0.054436

Transport

SNF8

Vacuolar sorting protein SNF8

XR_019363.1

0.000425

Uncharacterized

C14orf101

Uncharacterized protein C14orf101

NM_017799.3

0.02931

Uncharacterized

C16orf57

C16orf57 protein

NM_024598.2

0.000456

Uncharacterized

Q6PDB4

-

-

2.68E-05

Uncharacterized

Q6ZMS0

CDNA FLJ16729

-

0.027141

Uncharacterized

Q6ZRH2

CDNA FLJ46361

-

1.15E-06

Uncharacterized

Q8NB05

CDNA FLJ34424

-

0.000459

Uncharacterized

SEC14L5

-

XM_032693.5

2.77E-06

Uncharacterized

CD164L2

CD164 sialomucin-like 2 protein precursor

NM_207397.2

0.000576

Uncharacterized

CNOT6

CCR4-NOT transcription complex subunit

NM_015455.3

0.000838

Uncharacterized

Q6YL35

-

-

0.00218

Uncharacterized

Q8N2T9

CDNA: FLJ21438

XM_029084.8

0.007508

Uncharacterized

Q96NM1

CDNA FLJ30594

-

0.000447

Uncharacterized

C22orf30

Novel protein (DJ694E4.2 protein)

NM_173566.1

0.000611

Uncharacterized

SBDS

Shwachman-Bodian-Diamond syndrome

NM_016038.2

0.006543

Vision

ARSJ

arylsulfatase family, member J

NM_024590.3

0.000249

vision

OR51T1

Olfactory receptor 51T1

NM_001004759.1

0.000408

vision

OR6C1

Olfactory receptor 6C1

NM_001005182.1

0.000136

vision

DUSP5

Dual specificity protein phosphatase 5

NM_004419.3

0.000125

vision

OR5K1

Olfactory receptor 5K1 (HTPCRX10)

NM_001004736.2

0.000169

Vision

RPGR

retinitis pigmentosa GTPase regulator

NM_001023582.1

0.007569