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