TABLE 3.
Gene profiling analysis to identify candidate effectors of the alternative pathway
| Probe set identification no. | NCBIf accession no. | Description of gene product | Exp 1 results (induction [fold])
|
Exp 2 results (induction [fold])
|
|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IFNAR1−/− mock versus virus infected (AB-V1) | TD mock versus IFN-α/β treated (TD-IFN1) | TD-IFN1/AB-V1a | TD mock versus virus infected (TD-V1) | TD-V1/AB-V1b | IFNAR1−/− mock versus virus infected (AB-V2) | TD mock versus IFN-α/β treated (TD-IFN2) | TD-IFN2/AB-V2a | TD mock versus virus infected (TD-V2) | TD-V2/AB-V2b | ||||||||
| Fit criteria for candidate effector in two independent microarray experiments
|
|||||||||||||||||
| 103432_atc | AW122677 | ISG20 | 0.4 | 71.0 | 177.5 | 224.4 | 561.0 | 1.3 | 25.6 | 19.7 | 78.8 | 60.6 | |||||
| 104669_at | U73037 | IRF7 | 0.3 | 52.7 | 175.7 | 143.0 | 476.7 | 5.6 | 63.1 | 11.3 | 170.1 | 30.4 | |||||
| 98373_at | A1462516 | FcɛR | 0.2 | 29.2 | 146.0 | 117.8 | 589.0 | 0.2 | 59.7 | 298.5 | 184.8 | 924.0 | |||||
| 102906_at | L38444 | TGTP | 0.1 | 10.1 | 101.0 | 18.3 | 183.0 | 0.1 | 9.5 | 95.0 | 13.5 | 135.0 | |||||
| 96764_at | AJ007971 | IIGP | 0.4 | 37.0 | 92.5 | 68.6 | 171.5 | 0.7 | 25.5 | 36.4 | 37.3 | 53.3 | |||||
| 101436_at | M34815 | MIG | 0.4 | 35.5 | 88.8 | 362.0 | 905.0 | 7.6 | 33.8 | 4.4 | 680.3 | 89.5 | |||||
| 104750_at | M63630 | IRG-47 | 0.2 | 16.3 | 81.5 | 24.4 | 122.0 | 0.4 | 10.3 | 25.8 | 12.9 | 32.3 | |||||
| 95024_at | AW047653 | UBP43 | 2.8 | 162.0 | 57.9 | 467.9 | 167.1 | 1 | 26.7 | 26.7 | 71.0 | 71.0 | |||||
| 103066_at | L32973 | TKH | 3.9 | 107.6 | 27.6 | 243.9 | 62.5 | 22.9 | 173.6 | 7.6 | 354.6 | 15.5 | |||||
| 102879_sat | M31314 | FcγRI | 0.3 | 5.2 | 17.3 | 7.3 | 24.3 | 0.3 | 4.4 | 14.7 | 7.0 | 23.3 | |||||
| 160933_at | U53219 | IGTP | 0.8 | 12.3 | 15.4 | 30.1 | 37.6 | 0.6 | 16.3 | 27.2 | 37.3 | 62.2 | |||||
| 98410_at | AJ007972 | GTPI | 0.6 | 9.2 | 15.3 | 10.1 | 16.8 | 0.7 | 7.2 | 10.3 | 13.5 | 19.3 | |||||
| 93321_at | AF022371 | IFI203 | 1.1 | 16.2 | 14.7 | 31.1 | 28.3 | 1 | 30.9 | 30.9 | 41.1 | 41.1 | |||||
| 98417_at | M21038 | Mx1 | 22.9 | 272.5 | 11.9 | 484.4 | 21.2 | 34.5 | 97 | 2.8 | 148.1 | 4.3 | |||||
| 101876_sat | M35247 | MHC-17 | 0.6 | 6.8 | 11.3 | 12.7 | 21.2 | 0.7 | 6.7 | 9.6 | 11.0 | 15.7 | |||||
| 98472_at | Y00629 | MHC-23 | 0.8 | 9.0 | 11.3 | 13.4 | 16.8 | 0.9 | 8.5 | 9.4 | 12.8 | 14.2 | |||||
| 93949_at | M63658 | GBP-β4 | 0.4 | 4.1 | 10.3 | 9.9 | 24.8 | 0.7 | 3.1 | 4.4 | 7.9 | 11.3 | |||||
| 101465_at | U069240 | STAT-1 | 1.4 | 11.7 | 8.4 | 17.1 | 12.2 | 1.6 | 10.9 | 6.8 | 14.0 | 8.8 | |||||
| 100013_at | AW121732 | IFP35 | 1.0 | 8.2 | 8.2 | 11.1 | 11.1 | 0.8 | 8.4 | 10.5 | 13.6 | 17.0 | |||||
| 104177_at | AA204579 | Mvig | 25.8 | 207.9 | 8.1 | 501.5 | 19.4 | 54.9 | 203.7 | 3.7 | 347.3 | 6.3 | |||||
| 96533_at | AI508931 | Torsin 3A | 1.6 | 12.7 | 7.9 | 17.3 | 10.8 | 1.6 | 9.7 | 6.1 | 10.7 | 6.7 | |||||
| 93717_at | U50712 | MCP-5 | 0.7 | 5.4 | 7.7 | 9.3 | 13.3 | 1.6 | 7.7 | 4.8 | 11.6 | 7.3 | |||||
| 94162_at | D14859 | MVH | 1.6 | 11.2 | 7.0 | 25.3 | 15.8 | 0.8 | 7.4 | 9.3 | 28.2 | 35.3 | |||||
| 97409_at | U19119 | LRG-47 | 0.7 | 4.8 | 6.9 | 8.1 | 11.6 | 0.6 | 5.1 | 8.5 | 6.0 | 10.0 | |||||
| 103080_at | U15635 | Mg11 | 1.3 | 8.6 | 6.6 | 15.7 | 12.1 | 0.9 | 7.4 | 8.2 | 13.1 | 14.6 | |||||
| 94977_at | X15373 | IPR | 1.0 | 6.2 | 6.2 | 5.2 | 5.2 | 1.2 | 5.5 | 4.6 | 5.9 | 4.9 | |||||
| 101848_gat | AF040242 | Sp100 | 1.0 | 6.1 | 6.1 | 4.7 | 4.7 | 0.7 | 5.9 | 8.4 | 5.1 | 7.3 | |||||
| 93865_s_at | M35244 | MHC-10 | 1.1 | 5.8 | 5.3 | 12.7 | 11.5 | 1.1 | 5.4 | 4.9 | 8.6 | 7.8 | |||||
| 98030_at | J03776 | Rpt-1r | 1.5 | 7.9 | 5.3 | 9.6 | 6.4 | 1.1 | 5.6 | 5.1 | 7.1 | 6.5 | |||||
| 93956_at | U43086 | GARG-49 | 14.6 | 76.1 | 5.2 | 137.2 | 9.4 | 22.6 | 68.6 | 3.0 | 115.4 | 5.1 | |||||
| 103035_at | U60020 | TAP | 0.9 | 4.5 | 5.0 | 11.2 | 12.4 | 0.8 | 5.4 | 6.8 | 9.5 | 11.9 | |||||
| 98071_f_at | X77731 | DcK | 1.0 | 4.7 | 4.7 | 5.4 | 5.4 | 0.9 | 4.7 | 5.2 | 5.9 | 6.6 | |||||
| 161511_fat | AV152244 | ISG15 | 76.1 | 340.1 | 4.5 | 694.6 | 9.1 | 36 | 1,389.2 | 38.6 | 2,836.7 | 78.8 | |||||
| 93085_at | D44456 | LMP-2 | 1.1 | 4.8 | 4.4 | 6.3 | 5.7 | 1.1 | 5.7 | 5.2 | 7.4 | 6.7 | |||||
| 104597_at | AJ007970 | mGBP-2 | 6.7 | 26.9 | 4.0 | 37.0 | 5.5 | 9.5 | 26.5 | 2.8 | 37.3 | 3.9 | |||||
| 103254_at | AW049897 | FLN29 | 1.4 | 5.4 | 3.9 | 7.5 | 5.4 | 1.8 | 6 | 3.3 | 9.9 | 5.5 | |||||
| 103517_at | AA822898 | LySp100 | 12.3 | 43.7 | 3.6 | 222.9 | 18.1 | 1.2 | 66.7 | 5.6 | 222.9 | 18.6 | |||||
| 94112_at | U37522 | TRAIL | 2.4 | 7.3 | 3.0 | 16.1 | 6.7 | 1.4 | 26.2 | 18.7 | 79.9 | 57.1 | |||||
| 94774_at | M31418 | IFI202B | 2.8 | 8.1 | 2.9 | 16.3 | 5.8 | 2.9 | 6.6 | 2.3 | 9.6 | 3.3 | |||||
| 103639_at | U43085 | GARG-39 | 26.4 | 75.6 | 2.9 | 118.6 | 4.5 | 28.8 | 106.2 | 3.7 | 154.3 | 5.4 | |||||
| 97949_at | M16238 | FLP2 | 2.0 | 5.1 | 2.6 | 11.6 | 5.8 | 1.6 | 6.1 | 3.8 | 11.0 | 6.9 | |||||
| 98465_f_at | M31419 | IF1204 | 2.8 | 7.1 | 2.5 | 10.3 | 3.7 | 2.5 | 5 | 2.0 | 5.9 | 2.4 | |||||
| 92689_at | AB019505 | IL-18BP | 1.7 | 4.1 | 2.4 | 8.6 | 5.1 | 1 | 6.4 | 6.4 | 11.4 | 11.4 | |||||
| 93858_at | M33266 | IP-10 | 34.3 | 79.9 | 2.3 | 298.2 | 8.7 | 35.8 | 155.4 | 4.3 | 666.3 | 18.6 | |||||
| Fit criteria for candidate effector in microarray experiment 1
|
|||||||||||||||||
| 94224_s_atd | M74123 | IFI205 | 0.8 | 10.9 | 13.6 | 28.1 | 35.1 | 5.5 | 8.2 | 1.5 | 16.8 | 3.1 | |||||
| 98022_at | U48830 | PC-7 | 0.4 | 4.1 | 10.3 | 5.4 | 13.5 | ||||||||||
| 102279_at | AW046479 | UAE-E1 | 0.7 | 4.3 | 6.1 | 6.5 | 9.3 | 1.1 | 3.9 | 3.5 | 7.0 | 6.4 | |||||
| 161448_fat | AV355612 | LMP-7 | 0.7 | 4.2 | 6.0 | 5.2 | 7.4 | ||||||||||
| 161006_at | A1853978 | OAT | 1.6 | 8.2 | 5.1 | 12.7 | 7.9 | 2.1 | 2.9 | ||||||||
| 93942_at | U27295 | InPP | 1.2 | 6.0 | 5.0 | 9.9 | 8.3 | ||||||||||
| 160799_at | AW060549 | ENDO | 1.1 | 4.5 | 4.1 | 39.1 | 35.5 | 12.0 | |||||||||
| 101486_at | Y10875 | LMP-10 | 1.2 | 4.1 | 3.4 | 6.3 | 5.3 | 1.2 | 3.6 | 3.0 | 5.6 | 4.7 | |||||
| 97106_at | D13759 | CotK | 3.3 | 7.5 | 2.3 | 10.7 | 3.2 | ||||||||||
| 100981_at | U43084 | GARG16 | 80.4 | 182.3 | 2.3 | 319.6 | 4.0 | 390.7 | 130.7 | 0.3 | 199.5 | 0.5 | |||||
| 102965_at | AW121646 | LRP | 2.0 | 4.3 | 2.2 | 7.0 | 3.5 | 1.9 | 3.7 | 1.9 | 7.3 | 3.8 | |||||
| Fit criteria for candidate effector in microarray experiment 2
|
|||||||||||||||||
| 160393_ate | AI853226 | EST | 0.6 | 3.1 | 5.5 | 4.8 | 8.6 | 0.7 | 4 | 5.7 | 5.5 | 7.9 | |||||
| 160965_at | AA163960 | EST | 1.5 | 3.6 | 2.4 | 5.5 | 3.6 | 2 | 4.7 | 2.4 | 7.2 | 3.6 | |||||
| 104713_at | AA863717 | N6MT | 1.3 | 2.7 | 2.1 | 6.1 | 4.8 | 1.3 | 4.4 | 3.4 | 7.7 | 5.9 | |||||
| 103202_at | AW047476 | EST | 12.2 | 20.3 | 1.7 | 36.3 | 3.0 | 13.4 | 28.4 | 2.1 | 43.1 | 3.2 | |||||
| 103443_at | AA711704 | EST | 2.4 | 3.4 | 1.4 | 8.1 | 3.3 | 2 | 4 | 2.0 | 12.2 | 6.1 | |||||
| 102699_at | J03368 | EST | 2.4 | 3.1 | 1.3 | 6.7 | 2.8 | 2 | 6.5 | 3.3 | 21.7 | 10.9 | |||||
| 95303_at | AA144469 | 1-8U | 2.1 | 0.4 | 10.6 | 26.5 | 10.5 | 26.3 | |||||||||
| 98283_at | X91617 | mxRN1p | 3.4 | 0.6 | 4.8 | 8.0 | 6.1 | 10.2 | |||||||||
| 104456_at | AAA863742 | EST | 2.3 | 1.8 | 4.1 | 2.3 | 5.2 | 2.9 | |||||||||
a
To determine whether genes were upregulated at least twofold over virus-infected IFNAR1−/− in IFN-α/β-primed TD BMDC, upregulation in IFN-α/β-primed TD was divided by upregulation in virus-infected IFNAR1−/− BMDC.
b
To determine whether genes were upregulated at least twofold over virus-infected IFNAR1−/− in virus-infected TD BMDC, upregulation in IFN-α/β-primed TD was divided by upregulation in virus-infected IFNAR1−/− BMDC.
c
Data in the first group are fit criteria for candidate effectors in two independent microarray experiments.
d
Data in the second group are fit criteria for candidate effectors in microarray experiment 1.
e
Data in the third group are fit criteria for candidate effectors in microarray experiment 2.
f
NCBI, National Center for Biotechnology Information.