TABLE 4.

Change in gene expressiona

Function/descriptionResponseSymbolFold change in gene expression on day:
1271428
Antiviral response
    Interferon-stimulated gene 20 kDaMarkedISG203.212.492.212.072.16
    Interferon-stimulated gene 20 kDaPoorISG202.752.111.651.501.57
    2′5′-Oligoadenylate synthetase 1 (40/46 kDa)MarkedOAS17.036.784.183.804.29
    2′5′-Oligoadenylate synthetase 1 (40/46 kDa)PoorOAS14.944.862.822.983.01
    2′5′-Oligoadenylate synthetase 2 (69/71 kDa)MarkedOAS25.104.913.884.044.44
    2′5′-Oligoadenylate synthetase 2 (69/71 kDa)PoorOAS23.673.552.572.632.77
    2′5′-Oligoadenylate synthetase-likeMarkedOASL7.836.723.574.094.16
    2′5′-Oligoadenylate synthetase-likePoorOASL5.564.942.642.632.99
    Viperin, cig5MarkedRSAD218.6417.9410.314.2815.58
    Viperin, cig 5PoorRSAD212.1112.16.707.137.66
Apoptosis
    XIAP associated factor 1MarkedHSXIAPAF13.484.003.423.743.52
    XIAP associated factor 1PoorHSXIAPAF12.872.992.362.412.56
    TRAILMarkedTNFSF105.44.332.312.162.42
    TRAILPoorTNFSF103.282.99 1.56 1.59 1.67
Cell proliferation
    Lysosomal-associated membrane protein 3MarkedLAMP311.526.615.55.136.19
    Lysosomal-associated membrane protein 3PoorLAMP37.184.572.782.693.45
Chemokines
    Chemokine (C-C motif) ligand 2MarkedCCL25841.0716.2423.5915.65
    Chemokine (C-C motif) ligand 2PoorCCL2 52.43 27.33 7.07 75.62 10.38
    Chemokine (C-C motif) receptor 1MarkedCCR14.223.882.212.862.82
    Chemokine (C-C motif) receptor 1PoorCCR12.84 2.86 1.78 2.08 1.84
    Chemokine (C-C motif) ligand 8MarkedCCL811.185.282.012.472.85
    Chemokine (C-C motif) ligand 8PoorCCL8 7.04 2.70 1.40 1.57 1.56
    Chemokine (C-X-C motif) ligand 11MarkedCXCL115.092.22 −1.01 1.00 −1.07
    Chemokine (C-X-C motif) ligand 11PoorCXCL114.83 2.66 3.66 1.33 1.22
    Chemokine (C-X-C motif) ligand 10MarkedCXCL1024.4211.881.791.932.00
    Chemokine (C-X-C motif) ligand 10PoorCXCL1019.958.941.51 1.47 1.56
Complement pathway
    Complement component 3a receptor 1MarkedC3AR13.623.281.762.221.92
    Complement component 3a receptor 1PoorC3AR12.382.32 1.35 1.49 1.33
    Serine (or cysteine) proteinase inhibitorMarkedSERPING111.937.092.192.57 2.43
    Serine (or cysteine) proteinase inhibitorPoorSERPING18.885.651.942.292.24
Endonuclease
    Liver RNase (neurotoxin)MarkedRNAse22.852.702.102.712.24
    Liver RNase (neurotoxin)PoorRNAse22.192.13 1.74 1.64 1.82
Helicases
    Hypothetical protein FLJ20035MarkedFLJ200354.564.384.104.064.27
    Hypothetical protein FLJ20035PoorFLJ200353.362.852.422.162.66
    Interferon induced with helicase C domain 1MarkedIFIH15.594.993.523.704.21
    Interferon induced with helicase C domain 1PoorIFIH13.593.252.242.202.48
Immune response
    Alpha interferon-inducible protein (clone IFI-15K)MarkedG1P210.519.766.537.728.35
    Alpha interferon-inducible protein (clone IFI-15K)PoorG1P27.436.933.894.244.75
    Alpha interferon-inducible protein (clone IFI-6-16)MarkedG1P34.114.093.023.223.07
    Alpha interferon-inducible protein (clone IFI-6-16)PoorG1P33.392.67 1.73 1.992.29
    Alpha interferon-inducible protein 27MarkedIFI2727.9841.5461.26100.47121.84
    Alpha interferon-inducible protein 27PoorIFI2721.4535.2852.6769.5189.4
    Interferon-induced protein 35MarkedIFI354.754.182.772.582.71
    Interferon-induced protein 35PoorIFI353.563.00 1.82 1.87 1.95
    Interferon-induced protein 44MarkedIFI446.626.316.036.596.77
    Interferon-induced protein 44PoorIFI444.294.123.413.364.09
    Interferon-induced protein 44MarkedIFI44L9.099.369.1310.6810.67
    Interferon-induced protein 44PoorIFI44L5.915.935.024.956.06
    Interferon-induced protein with tetratricopeptide repeats 1MarkedIFIT117.5717.110.7212.2713.55
    Interferon-induced protein with tetratricopeptide repeats 1PoorIFIT19.239.235.795.276.31
    Interferon-induced protein with tetratricopeptide repeats 3MarkedIFIT311.9510.36.387.538.47
    Interferon-induced protein with tetratricopeptide repeats 3PoorIFIT37.426.733.563.744.23
    Interferon-induced protein with tetratricopeptide repeats 5MarkedIFIT53.323.192.632.722.94
    Interferon-induced protein with tetratricopeptide repeats 5PoorIFIT52.492.302.052.022.00
    Interferon-induced transmembrane protein 1 (9-27)MarkedIFITM11.861.761.671.711.95
    Interferon induced transmembrane protein 1 (9-27)PoorIFITM11.711.63 1.42 1.41 1.62
    Interferon-induced transmembrane protein 3 (1-8U)MarkedIFITM32.712.451.892.001.91
    Interferon-induced transmembrane protein 3 (1-8U)PoorIFITM32.282.201.601.651.82
    IL-1 receptor antagonistMarkedIL1RN5.834.12 1.43 1.99 1.98
    IL-1 receptor antagonistPoorIL1RN4.212.93 1.44 2.051.75
    Myxovirus (influenza virus) resistance 1MarkedMX16.515.804.955.575.39
    Myxovirus (influenza virus) resistance 1PoorMX14.293.902.832.873.26
    Myxovirus (influenza virus) resistance 2MarkedMX24.393.893.073.283.30
    Myxovirus (influenza virus) resistance 2PoorMX23.462.942.042.122.49
Inflammatory response
    HeparanaseMarkedHPSE4.162.451.732.051.80
    HeparanasePoorHPSE2.971.92 1.39 1.501.59
    SialoadhesinMarkedSN44.5439.6523.1433.5826.4
    SialoadhesinPoorSN18.1716.459.3711.9212.41
JAK-STAT cascade
    N-myc (and STAT) interactorMarkedNMI3.072.681.911.932.08
    N-myc (and STAT) interactorPoorNMI2.192.01 1.50 1.46 1.59
    Signal transducer and activator of transcription 1 (91 kDa)MarkedSTAT12.382.051.881.852.09
    Signal transducer and activator of transcription 1 (91 kDa)PoorSTAT11.981.77 1.46 1.37 1.61
Phospholipid scrambling
    Phospholipid scramblase 1MarkedPLSCR14.614.222.923.323.50
    Phospholipid scramblase 1PoorPLSCR13.242.97 2.17 2.012.50
RNA editing
    Apolipoprotein B mRNA editing enzymeMarkedAPOBEC3A6.034.662.632.932.94
    Apolipoprotein B mRNA editing enzymePoorAPOBEC3A4.293.532.082.152.22
Signal transduction
    Membrane-spanning 4 domains, subfamily A, member 4MarkedMS4A4A7.007.362.352.892.48
    Membrane-spanning 4 domains, subfamily A, member 4PoorMS4A4A3.684.39 1.61 1.71 1.89
Toll pathway
    Toll-like receptor 7MarkedTLR77.175.122.903.192.79
    Toll-like receptor 7PoorTLR73.933.07 1.70 1.66 1.80
Transcription factor/repressor
    CD38 antigen (p45)MarkedCD382.612.151.891.861.90
    CD38 antigen (p45)PoorCD382.432.031.64 1.46 1.56
    Homeobox (expressed in ES cells) 1MarkedHESX123.0117.49.4410.469.53
    Homeobox (expressed in ES cells) 1PoorHESX117.5612.78 9.01 5.746.23
    Gamma interferon-inducible protein 16MarkedIFI162.282.051.941.801.80
    Gamma interferon-inducible protein 16PoorIFI161.841.871.55 1.45 1.51
    Interferon regulatory factor 7MarkedIRF74.564.253.123.203.37
    Interferon regulatory factor 7PoorIRF73.343.112.042.192.33
    Lectin, galactoside-binding, soluble, 9 (galectin 9)MarkedLGALS93.042.861.861.812.07
    Lectin, galactoside-binding, soluble, 9 (galectin 9)PoorLGALS92.302.07 1.32 1.61 1.65
    Lymphocyte antigen 6 complex, locus EMarkedLY6E4.594.933.683.313.85
    Lymphocyte antigen 6 complex, locus EPoorLY6E3.713.71 2.25 2.95 2.86
    Nuclear antigen Sp100MarkedSP1002.041.901.891.821.75
    Nuclear antigen Sp100PoorSP1001.781.781.51 1.37 1.43
    SP110 nuclear body proteinMarkedSP1101.982.031.761.801.85
    SP110 nuclear body proteinPoorSP1101.641.64 1.46 1.46 1.53
    T-box 3 (ulnar mammary syndrome)MarkedTBX37.366.134.264.424.42
    T-box 3 (ulnar mammary syndrome)PoorTBX34.914.022.472.352.6
Ubiquitin pathway
    Hect domain and RLD 5MarkedHERC58.647.504.645.065.46
    Hect domain and RLD 5PoorHERC55.925.092.882.853.18
    Hect domain and RLD 6MarkedHERC65.615.465.845.545.61
    Hect domain and RLD 6PoorHERC64.194.073.593.353.76
    Promyelocytic leukemiaMarkedPML3.682.891.801.931.91
    Promyelocytic leukemiaPoorPML3.072.26 1.49 1.601.60
    Ubiquitin-conjugating enzyme E2L 6MarkedUBE2L62.972.521.761.811.82
    Ubiquitin-conjugating enzyme E2L 6PoorUBE2L62.542.19 1.42 1.45 1.53
    Ubiquitin-specific protease 18MarkedUSP1812.5310.067.108.669.96
    Ubiquitin-specific protease 18PoorUSP186.895.804.003.954.89
Unknown function
    28-kDa interferon-responsive proteinMarkedIFRG284.684.873.383.523.76
    28-kDa interferon-responsive proteinPoorIFRG283.433.09 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.