TABLE 2.
Expression profiles of reovirus-regulated genesa
| Cluster and gene symbol | GenBank accession no. | Mean scaled avg difference
|
Pr(F)
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| NF-κB intact (+Dox)
|
NF-κB inhibited (−Dox)
|
NF-κB (+Dox) | Reovirus | ||||||||
| 0 h | 2 h | 6 h | 10 h | 0 h | 2 h | 6 h | 10 h | ||||
| Cluster I | |||||||||||
| POLD1 | M80397 | 80 | 67 | 67 | 62 | 802 | 73 | 69 | 77 | 4.81E-08 | 5.73E-09 |
| CGA | S70585 | 6,909 | 8,097 | 6,852 | 6,705 | 8,215 | 9,129 | 8,553 | 8,277 | 6.00E-07 | 1.43E-04 |
| MFAP2 | U19718 | 4,730 | 4,359 | 3,853 | 3,466 | 6,048 | 5,222 | 4,759 | 4,718 | 7.00E-07 | 1.10E-05 |
| SLC9A8 | AL031685 | 80 | 67 | 67 | 62 | 233 | 73 | 69 | 77 | 1.65E-05 | 2.46E-06 |
| HR | W27191 | 80 | 67 | 67 | 62 | 269 | 73 | 69 | 77 | 1.94E-05 | 2.86E-06 |
| BAPX1 | AF009801 | 352 | 227 | 269 | 243 | 438 | 311 | 342 | 396 | 9.46E-05 | 1.30E-03 |
| ERCC4 | L76568 | 80 | 67 | 67 | 62 | 76 | 304 | 69 | 77 | 4.93E-04 | 1.74E-04 |
| POU6F1 | Z21966 | 80 | 67 | 67 | 62 | 93 | 165 | 69 | 77 | 1.02E-03 | 2.39E-03 |
| LMO1 | M26682 | 554 | 309 | 335 | 384 | 916 | 390 | 419 | 481 | 1.09E-03 | 8.32E-05 |
| INSIG1 | U96876 | 373 | 372 | 184 | 190 | 558 | 484 | 184 | 333 | 1.11E-03 | 5.14E-05 |
| RAB5B | X54871 | 479 | 394 | 353 | 342 | 564 | 487 | 395 | 507 | 1.46E-03 | 5.88E-03 |
| ARL3 | AF038193 | 80 | 67 | 67 | 62 | 179 | 73 | 69 | 77 | 1.83E-03 | 4.41E-04 |
| HBP1 | AF019214 | 299 | 265 | 124 | 186 | 419 | 283 | 148 | 189 | 2.17E-03 | 6.93E-07 |
| PPP1R3C | N36638 | 242 | 308 | 228 | 184 | 334 | 474 | 263 | 244 | 2.18E-03 | 1.22E-03 |
| ACADS | Z80345 | 80 | 67 | 67 | 62 | 234 | 73 | 106 | 77 | 2.37E-03 | 2.96E-03 |
| CLK3 | L29217 | 388 | 282 | 262 | 283 | 354 | 290 | 69 | 242 | 2.85E-03 | 1.00E-04 |
| RABGGTA | Y08200 | 389 | 365 | 380 | 404 | 405 | 373 | 69 | 372 | 2.99E-03 | 6.17E-04 |
| IL10RB | AI984234 | 458 | 404 | 408 | 397 | 643 | 537 | 415 | 450 | 3.06E-03 | 9.20E-03 |
| FOS | V01512 | 928 | 1,283 | 778 | 156 | 1,018 | 1,972 | 853 | 263 | 3.12E-03 | 1.02E-06 |
| MTUS1 | AL096842 | 392 | 310 | 268 | 315 | 513 | 419 | 291 | 392 | 6.13E-03 | 4.27E-03 |
| ARMC6 | AC003038 | 697 | 675 | 67 | 62 | 330 | 73 | 69 | 77 | 6.65E-03 | 2.70E-03 |
| SMAD2 | U68018 | 671 | 852 | 688 | 735 | 814 | 962 | 702 | 851 | 7.99E-03 | 3.14E-03 |
| LAMA4 | S78569 | 118 | 97 | 79 | 79 | 176 | 134 | 98 | 98 | 8.02E-03 | 7.02E-03 |
| CLDN7 | AJ011497 | 245 | 185 | 146 | 152 | 286 | 225 | 180 | 229 | 8.11E-03 | 4.25E-03 |
| DDR1 | L20817 | 381 | 378 | 330 | 248 | 477 | 445 | 294 | 341 | 8.37E-03 | 5.99E-04 |
| HTRA1 | D87258 | 1,510 | 1,404 | 1,194 | 950 | 1,776 | 1,822 | 1,289 | 1,369 | 9.24E-03 | 8.39E-03 |
| NOTCH3 | U97669 | 708 | 474 | 383 | 320 | 815 | 692 | 417 | 463 | 9.53E-03 | 3.03E-04 |
| CHES1 | U68723 | 364 | 301 | 308 | 330 | 508 | 355 | 319 | 383 | 9.54E-03 | 8.58E-03 |
| HYAL1 | U03056 | 370 | 224 | 148 | 124 | 443 | 243 | 133 | 181 | 9.90E-03 | 2.10E-07 |
| Cluster II (kinetic class 3) | |||||||||||
| IRF1 | L05072 | 80 | 67 | 619 | 664 | 76 | 73 | 69 | 77 | 8.10E-11 | 7.18E-10 |
| OAS1 (p40/46) | X04371 | 80 | 67 | 67 | 846 | 76 | 73 | 69 | 77 | 1.76E-10 | 1.69E-11 |
| TNIP1 | AJ011896 | 80 | 67 | 1,138 | 1,290 | 76 | 73 | 69 | 77 | 9.47E-08 | 8.07E-07 |
| G1P2 | AA203213 | 79.5 | 194 | 661 | 3,472 | 76 | 73 | 553 | 1,620 | 3.03E-07 | 1.79E-11 |
| CCL5 | M21121 | 80 | 67 | 267 | 692 | 76 | 73 | 69 | 225 | 2.45E-06 | 1.46E-07 |
| IRF7 | U53831 | 80 | 67 | 67 | 631 | 76 | 73 | 69 | 183 | 3.88E-06 | 1.88E-08 |
| G1P3 | U22970 | 80 | 67 | 67 | 1,260 | 76 | 73 | 69 | 406 | 5.97E-06 | 7.80E-09 |
| STAT1 | M97936 | 261 | 265 | 391 | 1,457 | 301 | 264 | 303 | 443 | 1.75E-05 | 1.75E-06 |
| MX2 | M30818 | 80 | 67 | 67 | 236 | 76 | 73 | 69 | 75 | 4.15E-05 | 3.44E-06 |
| IFIT1 | M24594 | 110 | 98 | 1,090 | 7,793 | 99 | 99 | 864 | 3,164 | 6.20E-05 | 2.59E-08 |
| STAT2 | U18671 | 80 | 67 | 67 | 219 | 76 | 73 | 69 | 77 | 6.92E-05 | 4.37E-06 |
| OGFR | AF109134 | 1,545 | 1,636 | 1,543 | 3,024 | 1,385 | 1,329 | 1,140 | 1,485 | 1.09E-04 | 2.43E-04 |
| FXYD2 | H94881 | 80 | 67 | 67 | 62 | 76 | 73 | 69 | 187 | 1.26E-04 | 8.51E-05 |
| CXCL10 | X02530 | 80 | 67 | 62 | 226 | 76 | 73 | 69 | 77 | 1.54E-04 | 7.62E-06 |
| EBNA1BP2 | U86602 | 2,599 | 2,573 | 2,757 | 3,066 | 2,216 | 2,306 | 2,384 | 2,536 | 1.56E-04 | 5.24E-03 |
| PLSCR1 | AB006746 | 719 | 781 | 1,142 | 3,321 | 715 | 718 | 697 | 1,024 | 1.61E-04 | 2.75E-05 |
| CXCL11 | AF030514 | 80 | 67 | 90 | 437 | 76 | 73 | 69 | 80 | 1.92E-04 | 3.65E-05 |
| BF | L15702 | 80 | 67 | 365 | 415 | 76 | 73 | 69 | 77 | 3.28E-04 | 2.40E-03 |
| IFIT5 | U34605 | 140 | 163 | 206 | 452 | 162 | 134 | 181 | 229 | 3.53E-04 | 4.08E-06 |
| OASL (p59) | AJ225089 | 80 | 237 | 2,092 | 11,230 | 76 | 148 | 1,646 | 6,298 | 5.01E-04 | 1.82E-08 |
| NMI | U32849 | 578 | 446 | 497 | 954 | 495 | 468 | 388 | 504 | 6.54E-04 | 3.80E-04 |
| SP110 | L22342 | 80 | 67 | 67 | 413 | 76 | 73 | 69 | 77 | 8.88E-04 | 1.21E-04 |
| TDRD7 | AB025254 | 80 | 67 | 99 | 396 | 76 | 73 | 69 | 121 | 9.74E-04 | 4.87E-05 |
| FLJ38348 | AL047596 | 208 | 217 | 323 | 817 | 261 | 230 | 265 | 352 | 1.87E-03 | 2.16E-05 |
| TAP1 | X57522 | 434 | 332 | 554 | 916 | 316 | 290 | 406 | 415 | 1.93E-03 | 2.42E-03 |
| IFITM1 | J04164 | 1,730 | 1,477 | 1,376 | 4,210 | 1,641 | 1,524 | 1,202 | 1,451 | 2.31E-03 | 8.63E-04 |
| TUBB4 | U47634 | 3,747 | 3,720 | 3,899 | 4,407 | 2,979 | 3,247 | 3,409 | 3,942 | 2.69E-03 | 9.33E-03 |
| PML | M82827 | 174 | 67 | 163 | 817 | 76 | 73 | 69 | 77 | 2.80E-03 | 4.24E-03 |
| PODXL | U97519 | 887 | 881 | 1,224 | 1,259 | 805 | 752 | 987 | 1,019 | 3.29E-03 | 8.79E-04 |
| IL15 | AF031167 | 148 | 138 | 274 | 330 | 168 | 144 | 212 | 155 | 3.84E-03 | 7.45E-04 |
| PTGES | AF010316 | 427 | 879 | 1,145 | 1,148 | 76 | 73 | 846 | 1,060 | 4.30E-03 | 7.21E-04 |
| TRIM21 | M62800 | 160 | 176 | 231 | 795 | 223 | 174 | 115 | 231 | 4.83E-03 | 7.46E-04 |
| RAD51C | AF029669 | 307 | 205 | 234 | 179 | 262 | 164 | 144 | 176 | 6.85E-03 | 8.24E-04 |
| IFI16 | M63838 | 618 | 469 | 417 | 1,565 | 517 | 504 | 370 | 524 | 7.21E-03 | 1.97E-03 |
| HEG1 | W28612 | 861 | 949 | 1,452 | 1,690 | 732 | 956 | 1,143 | 1,173 | 7.66E-03 | 5.03E-04 |
| IFIT2 | M14660 | 80 | 67 | 562 | 4,647 | 76 | 73 | 681 | 2,518 | 7.73E-03 | 2.97E-07 |
| DPH2 | AF053003 | 964 | 1,061 | 1,201 | 1,229 | 912 | 929 | 1,127 | 1,079 | 8.63E-03 | 1.22E-03 |
| GSTM3 | J05459 | 458 | 340 | 418 | 348 | 345 | 73 | 423 | 384 | 8.90E-03 | 1.04E-03 |
| ANXA3 | M20560 | 311 | 352 | 546 | 683 | 205 | 233 | 447 | 475 | 9.01E-03 | 9.48E-04 |
| LHFPL2 | D86961 | 522 | 414 | 553 | 582 | 591 | 474 | 576 | 615 | 9.30E-03 | 2.10E-04 |
| UBC | AB009010 | 4,699 | 4,354 | 4,769 | 5,500 | 5,370 | 4,746 | 5,423 | 5,881 | 9.33E-03 | 5.68E-03 |
| IFI44 | D28915 | 170 | 211 | 758 | 2,453 | 156 | 162 | 618 | 1,452 | 9.84E-03 | 1.81E-06 |
| Cluster III (kinetic class 1) | |||||||||||
| IL6 | X04430 | 80 | 1,222 | 1,116 | 759 | 76 | 355 | 235 | 180 | 2.44E-08 | 3.85E-07 |
| CXCL2 | M36820 | 46 | 395 | 205 | 204 | 76 | 139 | 105 | 79 | 5.01E-07 | 5.68E-07 |
| PLK3 | U56998 | 80 | 869 | 67 | 62 | 76 | 73 | 69 | 77 | 1.35E-06 | 1.41E-07 |
| TNFAIP3 | M59465 | 132 | 742 | 588 | 380 | 91 | 350 | 190 | 183 | 7.00E-06 | 1.25E-05 |
| PSMB9 | AA808961 | 370 | 318 | 321 | 646 | 268 | 218 | 221 | 199 | 1.47E-05 | 1.99E-03 |
| NFKBIA | M69043 | 706 | 2,079 | 1,664 | 1,126 | 717 | 1,340 | 953 | 627 | 1.04E-04 | 2.77E-05 |
| IL8 | M28130 | 80 | 1,866 | 580 | 62 | 76 | 421 | 69 | 77 | 2.61E-04 | 3.12E-05 |
| CXCL1 | X54489 | 117 | 615 | 341 | 162 | 76 | 351 | 69 | 77 | 3.67E-04 | 3.71E-05 |
| GADD45A | M60974 | 362 | 687 | 563 | 430 | 392 | 538 | 422 | 398 | 3.93E-04 | 4.73E-06 |
| NFKB1 | M58603 | 2,747 | 3,708 | 4,029 | 3,044 | 2,836 | 2,802 | 2,908 | 2,515 | 5.40E-04 | 5.02E-03 |
| IFNGR1 | U19247 | 297 | 479 | 480 | 362 | 282 | 372 | 321 | 234 | 5.83E-04 | 1.48E-03 |
| CCND1 | M64349 | 1,097 | 1,339 | 1,452 | 917 | 1,009 | 1,106 | 946 | 800 | 5.89E-04 | 1.17E-03 |
| PLK2 | AF059617 | 68 | 736 | 382 | 185 | 76 | 419 | 198 | 125 | 7.35E-04 | 3.84E-06 |
| IFITM3 | X57352 | 9,310 | 9,027 | 8,522 | 15,241 | 7,661 | 6,352 | 7,720 | 8,288 | 9.43E-04 | 4.63E-03 |
| TNFAIP2 | M92357 | 1,029 | 1,560 | 1,619 | 880 | 943 | 1,252 | 1,028 | 822 | 1.11E-03 | 1.90E-04 |
| PLAUR | U09937 | 1,112 | 2,347 | 1,785 | 2,146 | 1,028 | 2,106 | 1,644 | 1,529 | 1.74E-03 | 5.26E-06 |
| JUNB | M29039 | 573 | 1,466 | 1,031 | 772 | 589 | 1,175 | 918 | 456 | 1.94E-03 | 2.68E-06 |
| IL4R | X52425 | 168 | 365 | 360 | 192 | 148 | 274 | 224 | 100 | 2.47E-03 | 3.57E-04 |
| TNFAIP8 | AF099935 | 526 | 729 | 675 | 534 | 553 | 625 | 479 | 502 | 2.65E-03 | 9.96E-04 |
| RND3 | S82240 | 282 | 677 | 427 | 489 | 244 | 583 | 309 | 348 | 3.55E-03 | 3.15E-05 |
| PTPN1 | M93425 | 740 | 1,183 | 843 | 664 | 682 | 1,016 | 560 | 562 | 4.09E-03 | 8.53E-05 |
| EPHA2 | M59371 | 300 | 1,192 | 810 | 329 | 248 | 886 | 511 | 193 | 4.50E-03 | 1.26E-05 |
| PSCD1 | M85169 | 243 | 483 | 344 | 244 | 198 | 402 | 196 | 262 | 5.93E-03 | 7.12E-05 |
| IER3 | S81914 | 568 | 1,976 | 847 | 448 | 621 | 1,569 | 584 | 385 | 6.79E-03 | 1.40E-07 |
| ID1 | X77956 | 5,708 | 15,703 | 10,646 | 8,703 | 5,801 | 14,940 | 9,909 | 6,742 | 7.40E-03 | 1.00E-08 |
| BCAR3 | U92715 | 295 | 726 | 587 | 303 | 239 | 686 | 370 | 270 | 8.29E-03 | 4.96E-06 |
| AMIGO2 | AC004010 | 172 | 698 | 483 | 286 | 152 | 633 | 385 | 237 | 8.84E-03 | 1.00E-07 |
| CEBPD | M83667 | 577 | 1,440 | 903 | 931 | 557 | 1,202 | 611 | 660 | 8.89E-03 | 1.18E-04 |
| Cluster IV (kinetic class 2) | |||||||||||
| PLAU | X02419 | 296 | 902 | 1,034 | 586 | 254 | 707 | 705 | 412 | 1.06E-06 | 5.40E-09 |
| NFKB2 | U20816 | 80 | 306 | 431 | 328 | 76 | 73 | 69 | 77 | 1.74E-06 | 6.60E-04 |
| RHOB | M12174 | 652 | 1,257 | 1,242 | 1,605 | 903 | 1,522 | 1,957 | 1,839 | 3.65E-05 | 1.80E-06 |
| RELB | M83221 | 80 | 421 | 623 | 422 | 76 | 203 | 69 | 77 | 1.23E-04 | 6.86E-03 |
| SDC4 | D79206 | 169 | 524 | 672 | 503 | 202 | 431 | 353 | 251 | 5.10E-04 | 1.53E-04 |
| MAFF | AL021977 | 80 | 370 | 131 | 65 | 76 | 187 | 79 | 77 | 9.11E-04 | 2.80E-06 |
| TRIM16 | AF096870 | 729 | 1,163 | 1,908 | 1,686 | 767 | 832 | 1,161 | 1,022 | 3.43E-03 | 2.80E-03 |
| GALNT1 | U41514 | 355 | 418 | 444 | 424 | 333 | 359 | 365 | 403 | 3.57E-03 | 9.82E-03 |
| OSMR | U60805 | 323 | 540 | 597 | 552 | 340 | 473 | 481 | 362 | 3.89E-03 | 8.06E-04 |
| JUN | J04111 | 116 | 182 | 171 | 140 | 89 | 250 | 209 | 157 | 4.13E-03 | 4.81E-06 |
| TXNRD1 | X91247 | 3,421 | 4,352 | 5,620 | 4,496 | 3,151 | 4,230 | 4,786 | 3,948 | 4.67E-03 | 2.00E-05 |
| BIRC2 | U37547 | 251 | 443 | 548 | 474 | 249 | 392 | 391 | 359 | 7.50E-03 | 7.38E-04 |
| NPR3 | M59305 | 586 | 787 | 861 | 835 | 744 | 832 | 885 | 973 | 8.85E-03 | 1.00E-03 |
a
Shown are reovirus-responsive, NF-κB-dependent genes identified in the microarray analysis, categorized by gene cluster and kinetic class. The gene symbol, GenBank accession number, mean scaled average difference values for each treatment condition, and the P value [Pr(F)] as a function of either NF-κB signaling or reovirus infection are shown for each gene identified. Dox, doxycycline. Within each cluster, genes are listed according to statistical significance for NF-κB dependence.