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. 2007 Jan 31;81(7):3391–3401. doi: 10.1128/JVI.02640-06

TABLE 4.

Change in gene expressiona

Function/description Response Symbol Fold change in gene expression on day:
1 2 7 14 28
Antiviral response
    Interferon-stimulated gene 20 kDa Marked ISG20 3.21 2.49 2.21 2.07 2.16
    Interferon-stimulated gene 20 kDa Poor ISG20 2.75 2.11 1.65 1.50 1.57
    2′5′-Oligoadenylate synthetase 1 (40/46 kDa) Marked OAS1 7.03 6.78 4.18 3.80 4.29
    2′5′-Oligoadenylate synthetase 1 (40/46 kDa) Poor OAS1 4.94 4.86 2.82 2.98 3.01
    2′5′-Oligoadenylate synthetase 2 (69/71 kDa) Marked OAS2 5.10 4.91 3.88 4.04 4.44
    2′5′-Oligoadenylate synthetase 2 (69/71 kDa) Poor OAS2 3.67 3.55 2.57 2.63 2.77
    2′5′-Oligoadenylate synthetase-like Marked OASL 7.83 6.72 3.57 4.09 4.16
    2′5′-Oligoadenylate synthetase-like Poor OASL 5.56 4.94 2.64 2.63 2.99
    Viperin, cig5 Marked RSAD2 18.64 17.94 10.3 14.28 15.58
    Viperin, cig 5 Poor RSAD2 12.11 12.1 6.70 7.13 7.66
Apoptosis
    XIAP associated factor 1 Marked HSXIAPAF1 3.48 4.00 3.42 3.74 3.52
    XIAP associated factor 1 Poor HSXIAPAF1 2.87 2.99 2.36 2.41 2.56
    TRAIL Marked TNFSF10 5.4 4.33 2.31 2.16 2.42
    TRAIL Poor TNFSF10 3.28 2.99 1.56 1.59 1.67
Cell proliferation
    Lysosomal-associated membrane protein 3 Marked LAMP3 11.52 6.61 5.5 5.13 6.19
    Lysosomal-associated membrane protein 3 Poor LAMP3 7.18 4.57 2.78 2.69 3.45
Chemokines
    Chemokine (C-C motif) ligand 2 Marked CCL2 58 41.07 16.24 23.59 15.65
    Chemokine (C-C motif) ligand 2 Poor CCL2 52.43 27.33 7.07 75.62 10.38
    Chemokine (C-C motif) receptor 1 Marked CCR1 4.22 3.88 2.21 2.86 2.82
    Chemokine (C-C motif) receptor 1 Poor CCR1 2.84 2.86 1.78 2.08 1.84
    Chemokine (C-C motif) ligand 8 Marked CCL8 11.18 5.28 2.01 2.47 2.85
    Chemokine (C-C motif) ligand 8 Poor CCL8 7.04 2.70 1.40 1.57 1.56
    Chemokine (C-X-C motif) ligand 11 Marked CXCL11 5.09 2.22 −1.01 1.00 −1.07
    Chemokine (C-X-C motif) ligand 11 Poor CXCL11 4.83 2.66 3.66 1.33 1.22
    Chemokine (C-X-C motif) ligand 10 Marked CXCL10 24.42 11.88 1.79 1.93 2.00
    Chemokine (C-X-C motif) ligand 10 Poor CXCL10 19.95 8.94 1.51 1.47 1.56
Complement pathway
    Complement component 3a receptor 1 Marked C3AR1 3.62 3.28 1.76 2.22 1.92
    Complement component 3a receptor 1 Poor C3AR1 2.38 2.32 1.35 1.49 1.33
    Serine (or cysteine) proteinase inhibitor Marked SERPING1 11.93 7.09 2.19 2.57 2.43
    Serine (or cysteine) proteinase inhibitor Poor SERPING1 8.88 5.65 1.94 2.29 2.24
Endonuclease
    Liver RNase (neurotoxin) Marked RNAse2 2.85 2.70 2.10 2.71 2.24
    Liver RNase (neurotoxin) Poor RNAse2 2.19 2.13 1.74 1.64 1.82
Helicases
    Hypothetical protein FLJ20035 Marked FLJ20035 4.56 4.38 4.10 4.06 4.27
    Hypothetical protein FLJ20035 Poor FLJ20035 3.36 2.85 2.42 2.16 2.66
    Interferon induced with helicase C domain 1 Marked IFIH1 5.59 4.99 3.52 3.70 4.21
    Interferon induced with helicase C domain 1 Poor IFIH1 3.59 3.25 2.24 2.20 2.48
Immune response
    Alpha interferon-inducible protein (clone IFI-15K) Marked G1P2 10.51 9.76 6.53 7.72 8.35
    Alpha interferon-inducible protein (clone IFI-15K) Poor G1P2 7.43 6.93 3.89 4.24 4.75
    Alpha interferon-inducible protein (clone IFI-6-16) Marked G1P3 4.11 4.09 3.02 3.22 3.07
    Alpha interferon-inducible protein (clone IFI-6-16) Poor G1P3 3.39 2.67 1.73 1.99 2.29
    Alpha interferon-inducible protein 27 Marked IFI27 27.98 41.54 61.26 100.47 121.84
    Alpha interferon-inducible protein 27 Poor IFI27 21.45 35.28 52.67 69.51 89.4
    Interferon-induced protein 35 Marked IFI35 4.75 4.18 2.77 2.58 2.71
    Interferon-induced protein 35 Poor IFI35 3.56 3.00 1.82 1.87 1.95
    Interferon-induced protein 44 Marked IFI44 6.62 6.31 6.03 6.59 6.77
    Interferon-induced protein 44 Poor IFI44 4.29 4.12 3.41 3.36 4.09
    Interferon-induced protein 44 Marked IFI44L 9.09 9.36 9.13 10.68 10.67
    Interferon-induced protein 44 Poor IFI44L 5.91 5.93 5.02 4.95 6.06
    Interferon-induced protein with tetratricopeptide repeats 1 Marked IFIT1 17.57 17.1 10.72 12.27 13.55
    Interferon-induced protein with tetratricopeptide repeats 1 Poor IFIT1 9.23 9.23 5.79 5.27 6.31
    Interferon-induced protein with tetratricopeptide repeats 3 Marked IFIT3 11.95 10.3 6.38 7.53 8.47
    Interferon-induced protein with tetratricopeptide repeats 3 Poor IFIT3 7.42 6.73 3.56 3.74 4.23
    Interferon-induced protein with tetratricopeptide repeats 5 Marked IFIT5 3.32 3.19 2.63 2.72 2.94
    Interferon-induced protein with tetratricopeptide repeats 5 Poor IFIT5 2.49 2.30 2.05 2.02 2.00
    Interferon-induced transmembrane protein 1 (9-27) Marked IFITM1 1.86 1.76 1.67 1.71 1.95
    Interferon induced transmembrane protein 1 (9-27) Poor IFITM1 1.71 1.63 1.42 1.41 1.62
    Interferon-induced transmembrane protein 3 (1-8U) Marked IFITM3 2.71 2.45 1.89 2.00 1.91
    Interferon-induced transmembrane protein 3 (1-8U) Poor IFITM3 2.28 2.20 1.60 1.65 1.82
    IL-1 receptor antagonist Marked IL1RN 5.83 4.12 1.43 1.99 1.98
    IL-1 receptor antagonist Poor IL1RN 4.21 2.93 1.44 2.05 1.75
    Myxovirus (influenza virus) resistance 1 Marked MX1 6.51 5.80 4.95 5.57 5.39
    Myxovirus (influenza virus) resistance 1 Poor MX1 4.29 3.90 2.83 2.87 3.26
    Myxovirus (influenza virus) resistance 2 Marked MX2 4.39 3.89 3.07 3.28 3.30
    Myxovirus (influenza virus) resistance 2 Poor MX2 3.46 2.94 2.04 2.12 2.49
Inflammatory response
    Heparanase Marked HPSE 4.16 2.45 1.73 2.05 1.80
    Heparanase Poor HPSE 2.97 1.92 1.39 1.50 1.59
    Sialoadhesin Marked SN 44.54 39.65 23.14 33.58 26.4
    Sialoadhesin Poor SN 18.17 16.45 9.37 11.92 12.41
JAK-STAT cascade
    N-myc (and STAT) interactor Marked NMI 3.07 2.68 1.91 1.93 2.08
    N-myc (and STAT) interactor Poor NMI 2.19 2.01 1.50 1.46 1.59
    Signal transducer and activator of transcription 1 (91 kDa) Marked STAT1 2.38 2.05 1.88 1.85 2.09
    Signal transducer and activator of transcription 1 (91 kDa) Poor STAT1 1.98 1.77 1.46 1.37 1.61
Phospholipid scrambling
    Phospholipid scramblase 1 Marked PLSCR1 4.61 4.22 2.92 3.32 3.50
    Phospholipid scramblase 1 Poor PLSCR1 3.24 2.97 2.17 2.01 2.50
RNA editing
    Apolipoprotein B mRNA editing enzyme Marked APOBEC3A 6.03 4.66 2.63 2.93 2.94
    Apolipoprotein B mRNA editing enzyme Poor APOBEC3A 4.29 3.53 2.08 2.15 2.22
Signal transduction
    Membrane-spanning 4 domains, subfamily A, member 4 Marked MS4A4A 7.00 7.36 2.35 2.89 2.48
    Membrane-spanning 4 domains, subfamily A, member 4 Poor MS4A4A 3.68 4.39 1.61 1.71 1.89
Toll pathway
    Toll-like receptor 7 Marked TLR7 7.17 5.12 2.90 3.19 2.79
    Toll-like receptor 7 Poor TLR7 3.93 3.07 1.70 1.66 1.80
Transcription factor/repressor
    CD38 antigen (p45) Marked CD38 2.61 2.15 1.89 1.86 1.90
    CD38 antigen (p45) Poor CD38 2.43 2.03 1.64 1.46 1.56
    Homeobox (expressed in ES cells) 1 Marked HESX1 23.01 17.4 9.44 10.46 9.53
    Homeobox (expressed in ES cells) 1 Poor HESX1 17.56 12.78 9.01 5.74 6.23
    Gamma interferon-inducible protein 16 Marked IFI16 2.28 2.05 1.94 1.80 1.80
    Gamma interferon-inducible protein 16 Poor IFI16 1.84 1.87 1.55 1.45 1.51
    Interferon regulatory factor 7 Marked IRF7 4.56 4.25 3.12 3.20 3.37
    Interferon regulatory factor 7 Poor IRF7 3.34 3.11 2.04 2.19 2.33
    Lectin, galactoside-binding, soluble, 9 (galectin 9) Marked LGALS9 3.04 2.86 1.86 1.81 2.07
    Lectin, galactoside-binding, soluble, 9 (galectin 9) Poor LGALS9 2.30 2.07 1.32 1.61 1.65
    Lymphocyte antigen 6 complex, locus E Marked LY6E 4.59 4.93 3.68 3.31 3.85
    Lymphocyte antigen 6 complex, locus E Poor LY6E 3.71 3.71 2.25 2.95 2.86
    Nuclear antigen Sp100 Marked SP100 2.04 1.90 1.89 1.82 1.75
    Nuclear antigen Sp100 Poor SP100 1.78 1.78 1.51 1.37 1.43
    SP110 nuclear body protein Marked SP110 1.98 2.03 1.76 1.80 1.85
    SP110 nuclear body protein Poor SP110 1.64 1.64 1.46 1.46 1.53
    T-box 3 (ulnar mammary syndrome) Marked TBX3 7.36 6.13 4.26 4.42 4.42
    T-box 3 (ulnar mammary syndrome) Poor TBX3 4.91 4.02 2.47 2.35 2.6
Ubiquitin pathway
    Hect domain and RLD 5 Marked HERC5 8.64 7.50 4.64 5.06 5.46
    Hect domain and RLD 5 Poor HERC5 5.92 5.09 2.88 2.85 3.18
    Hect domain and RLD 6 Marked HERC6 5.61 5.46 5.84 5.54 5.61
    Hect domain and RLD 6 Poor HERC6 4.19 4.07 3.59 3.35 3.76
    Promyelocytic leukemia Marked PML 3.68 2.89 1.80 1.93 1.91
    Promyelocytic leukemia Poor PML 3.07 2.26 1.49 1.60 1.60
    Ubiquitin-conjugating enzyme E2L 6 Marked UBE2L6 2.97 2.52 1.76 1.81 1.82
    Ubiquitin-conjugating enzyme E2L 6 Poor UBE2L6 2.54 2.19 1.42 1.45 1.53
    Ubiquitin-specific protease 18 Marked USP18 12.53 10.06 7.10 8.66 9.96
    Ubiquitin-specific protease 18 Poor USP18 6.89 5.80 4.00 3.95 4.89
Unknown function
    28-kDa interferon-responsive protein Marked IFRG28 4.68 4.87 3.38 3.52 3.76
    28-kDa interferon-responsive protein Poor IFRG28 3.43 3.09 2.16 2.10 2.11
a

Changes in gene expression for marked responders and poor responders at days 1, 2, 7, 14, and 28 after initiation of treatment. Data were derived from Table S1 in the supplemental material. Numbers in boldface represent values below the cutoff of a 1.5-fold change or a P value of >0.001.