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Table 1 List of proteins up- or downregulated by two-fold or more by IFN in this study

From: System-based proteomic analysis of the interferon response in human liver cells

IPI code

Protein*

p †

Ratio‡

SD

Number§

IFN-induced proteins

IPI00164222

ACACA: acetyl-coenzyme A carboxylase alpha

1.00

3.351

0.259

2

IPI00033030¶

ADRM1: adhesion regulating molecule 1

0.79

9.508c

1.043

1

IPI00012007¶

AHCY: S-adenosylhomocysteine hydrolase

0.93

6.279n

0.936

1

IPI00032958

ANLN: anillin, actin binding protein (scraps homolog, Drosophila)

0.43

2.420

0.129

1

IPI00004656

B2M: beta-2-microglobulin

1.00

2.768

0.583

8

IPI00027803

BAL: B aggressive lymphoma gene

0.96

2.835

0.184

1

IPI00171487

CABC1: chaperone, ABC1 activity of bc1 complex like (S. pombe)

0.99

3.533

1.659

2

IPI00015199

CD7: CD7 antigen (p41)

0.57

4.523

2.204

2

IPI00028275

CH-TOG : Colonic and hepatic tumor overexpressed protein

1.00

2.048

0.085

4

IPI00011284

COMT: catechol-O-methyltransferase

1.00

2.614

0.239

2

IPI00164416

CSA_PPIasePeptidyl prolyl cis trans isomerase

1.00

8.104

1.070

55

IPI00029485

DCTN1: dynactin 1 (p150, glued homolog, Drosophila)

0.99

2.183

0.133

1

IPI00163553

DKFZP564C186: DKFZP564C186 protein

1.00

2.108

0.505

3

IPI00061170

DNAH11: dynein, axonemal, heavy polypeptide 11

0.94

9999

-1

2

IPI00015947

DNAJB1: DnaJ (Hsp40) homolog, subfmaily B, member 1

0.89

2.571

0.223

1

IPI00031836

DRG1: developmentally regulated GTP binding protein 1

1.00

2.471

1.588

4

IPI00029536

EEF1A protein [Fragment]

1.00

3.035

0.624

5

IPI00010810

ETFA: electron-transfer-flavoprotein, alpha polypeptide

0.45

2.890

0.484

1

IPI00065180

FLJ32915: hypothetical protein FLJ32915

0.73

6.054

4.883

2

IPI00031773

FOXA2: forkhead box A2, hepatic nuclear factor-3-beta

0.99

2.640

1.678

1

IPI00007241

G1P2: IFN, alpha-inducible protein (clone IFI-15K)

0.98

4.858

0.661

1

IPI00028564

GBP1: guanylate binding protein 1, IFN-inducible

0.56

2.130

0.208

1

IPI00026268 ¶

GNB1:G protein, beta subunit 1

1.00

5.845n

0.133

2

IPI00171038

GPR111: G protein-coupled receptor 111

0.63

21.27

4.741

2

IPI00007404

APG7L: ubiquitin activating enzyme E1-like protein, GSA7

0.98

2.844

0.663

1

IPI00007853

IFI30: IFN, gamma-inducible protein 30

0.97

2.219

0.183

1

IPI00008613

IFI35: IFN-induced protein 35

1.00

2.223

0.426

2

IPI00018300

IFIT1: IFN-induced protein with tetratricopeptide repeats 1

0.48

9999

-1

1

IPI00024254

IFIT4: IFN-induced protein with tetratricopeptide repeats 4

1.00

6.230

0.794

6

IPI00026834

INPP5E: inositol polyphosphate-5-phosphatase, 72 kDa

1.00

2.470

0.399

2

IPI00059811

ISG20: IFN stimulated gene 20 kDa

0.88

2.303

0.319

1

IPI00032387

KIAA0186: KIAA0186 gene product

0.99

2.365

0.198

2

IPI00003499

KIAA1276: KIAA1276 protein

0.62

3.815

0.058

1

IPI00020096

KNS2: kinesin 2 60/70 kDa

1.00

3.140

0.335

2

IPI00013976

LAMB1: laminin, beta 1

0.94

2.693

0.180

2

IPI00152503

LOC151636: rhysin 2

1.00

2.975

0.231

4

IPI00000421

M96:mouse metal response element binding transcription factor 2

0.98

2.923

0.390

1

IPI00023399

MTP: microsomal triglyceride transfer protein (88 kDa)

0.97

4.748

0.751

1

IPI00024681

MX1: myxovirus resistance 1, IFN-inducible protein p78

0.93

2.300

0.204

1

IPI00012450

NMI: N-Myc (and STAT) interactor

0.57

2.875

0.138

1

IPI00000022

NUDT2: nucleoside diphosphate linked moiety X type motif 2

0.98

3.684

0.224

2

IPI00002405

OAS3: 2'-5'-oligoadenylate synthetase 3, 100 kDa

1.00

2.460

0.076

5

IPI00141040

PASK PAS domain containing serine/threonine kinase

0.49

12.006

1.024

2

IPI00024989

PCMT1: protein-L-isoaspartate (D-aspartate) O-methyltransferase

0.98

2.836

0.276

1

IPI00016461

PLCD1: phospholipase C, delta 1

0.69

4.569

0.116

1

IPI00019463

PKR protein kinase, IFN-inducible ds RNA dependent

1.00

3.963

0.659

3

IPI00008530

RPLP0: ribosomal protein, large, P0

1.00

2.044

0.198

3

IPI00021417

SART1: T-cell recognized squamous cell carcinoma antigen

0.57

2.616

0.093

1

IPI00030781 ¶

STAT1: large peptide, 91 kDa

1.00

2.153 m

0.079

9

IPI00024723

UBE2L6: ubiquitin-conjugating enzyme E2L 6

0.57

9999

-1

1

IPI00146772

ENSEMBL:ENSP00000295676 Tax_Id = 9606

0.78

3.240

0.955

2

IPI00062913

REFSEQ:XP_062729 hypothetical protein

0.46

3.073

2.000

1

IPI00045468

REFSEQ:XP_058770 Hypothetical protein

0.47

2.675

0.113

1

IPI00145529

REFSEQ:XP_167245 similar to seven-pass transmembrane receptor protein precursor and cyclophilin type peptidylprolyl isomerase A

1.00

2.29

0.448

5

IFN-repressed proteins

IPI00009137

CPSF4: cleavage and polyadenylation specific factor 4, 30 kDa

0.96

0.378

0.154

1

IPI00024549

FABP: fatty acid binding protein

0.93

0.328

0.041

1

IPI00004619

FACL4: fatty-acid-coenzyme A ligase, long-chain 4

0.98

0.416

0.081

1

IPI00026781

FASN: fatty acid synthase

0.99

0.304

0.100

137

IPI00016250

FXR2: fragile X mental retardation, autosomal homolog 2

0.95

0.391

0.074

1

IPI00011454

G2AN: alpha glucosidase II alpha subunit

1.00

0.198

0.033

13

IPI00156282

GPS1: G protein pathway suppressor 1

0.98

0.455

0.138

1

IPI00150148

HIC1: hypermethylated in cancer 1

0.94

0.000

-1

1

IPI00015587

Hypothetical protein FLJ21140

0.71

0.043

0.064

3

IPI00166489

IGLC3: Ig lambda chain C regions

0.98

0.265

0.11

2

IPI00055954

KIAA0007: KIAA0007 protein

1.00

0.426

0.014

2

IPI00166105

KRT10: keratin 10

0.97

0.495

0.055

2

IPI00022980

KRT6: keratin 6

1.00

0.003

0.008

14

IPI00017596

MAPRE1: RP/EB family, member 1

0.98

0.339

0.016

1

IPI00005948

MGC3207: hypothetical protein MGC3207

0.61

0.499

0.071

1

IPI00004399

MIG-6: Gene 33/Mig-6

0.99

0.000

-1

2

IPI00022334

OAT: ornithine aminotransferase

0.98

0.331

0.018

1

IPI00021794

PPGB: protective protein for beta-galactosidase (galactosialidosis)

1.00

0.323

0.084

8

IPI00034308

SARDH: sarcosine dehydrogenase

0.98

0.484

0.008

1

IPI00023344

SYMPK: symplekin

1.00

0.496

0.029

3

IPI00099730

SRRM2: serine/arginine repetitive matrix 2

0.82

0.434

0.224

1

IPI00027230¶

TRA1: tumor rejection antigen (gp96) 1

1.00

0.452 mn

0.165

4

IPI00166768¶

TUBA6: tubulin alpha 6

1.00

0.383 m

0.165

14

IPI00024693

WNT9A: wingless-type MMTV integration site family, member 9A

0.99

0.316

0.091

2

  1. *Genes previously identified in the microarray study by Williams and colleagues [15] are shown in bold. †ProteinProphet probability score. ‡Ratio of IFN/mock. Ratio of 0.000 or 9999 indicates no detection of the IFN or mock signals, respectively. In either case the standard deviation is expressed as -1. §Number of peptides identified. ¶Proteins in which IFN-mediated expression was differentially regulated among the three cellular fractions in this study. Their ratios refer to specific cellular fractions as indicated: n, nuclear; m, membrane; c, cytoplasmic.
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Genome Biology

ISSN: 1474-760X

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