Table 4. Transfind transcription factor prediction.
| 36 hour upregulated | |||||||
| Factor | p-value | FDR | FP | # of genes + | # of genes - | Background + | Background - |
| E2F | <1.00E-07 | 3.000E-09 | 9.000E-09 | 45 | 331 | 955 | 32882 |
| NF-Y | 2.74E-07 | 1.486E-05 | 5.944E-05 | 31 | 345 | 969 | 32868 |
| HIF1 | 8.45E-07 | 3.057E-05 | 1.834E-04 | 30 | 346 | 970 | 32867 |
| GABP | 2.517E-06 | 6.827E-05 | 5.462E-04 | 29 | 347 | 971 | 32866 |
| CREBATF | 2.517E-06 | 6.827E-05 | 5.462E-04 | 29 | 347 | 971 | 32866 |
| STAT1 | 1.999E-05 | 4.338E-04 | 4.338E-03 | 27 | 349 | 973 | 32864 |
| CREB | 1.999E-05 | 4.338E-04 | 4.338E-03 | 27 | 349 | 973 | 32864 |
| CREBP1 | 5.322E-05 | 8.249E-04 | 1.155E-02 | 26 | 350 | 974 | 32863 |
| ATF4 | 5.322E-05 | 8.249E-04 | 1.155E-02 | 26 | 350 | 974 | 32863 |
| AHR | 5.322E-05 | 8.249E-04 | 1.155E-02 | 26 | 350 | 974 | 32863 |
| NFkB | 7.882E-04 | 1.069E-02 | 1.710E-01 | 23 | 353 | 977 | 32860 |
| YY1 | 7.882E-04 | 1.069E-02 | 1.710E-01 | 23 | 353 | 977 | 32860 |
| ATF2CJUN | 1.778E-03 | 1.930E-02 | 3.859E-01 | 22 | 354 | 978 | 32859 |
| C-REL | 1.778E-03 | 1.930E-02 | 3.859E-01 | 22 | 354 | 978 | 32859 |
| IRF1 | 1.778E-03 | 1.930E-02 | 3.859E-01 | 22 | 354 | 978 | 32859 |
| ATF3 | 1.778E-03 | 1.930E-02 | 3.859E-01 | 22 | 354 | 978 | 32859 |
| 36 hour downregulated | |||||||
| SP1 | <1.00E-09 | 3.000E-09 | 2.600E-08 | 85 | 781 | 915 | 32432 |
| WT1 | <1.00E-09 | 3.000E-09 | 2.600E-08 | 82 | 784 | 918 | 32429 |
| AP2 | <1.00E-09 | 3.000E-09 | 9.000E-09 | 81 | 785 | 919 | 32428 |
| TFIII | <1.00E-09 | 3.000E-09 | 2.600E-08 | 70 | 796 | 930 | 32417 |
| MAZ | <1.00E-09 | 3.000E-09 | 2.600E-08 | 69 | 797 | 931 | 32416 |
| HIC1 | <1.00E-09 | 3.000E-09 | 2.600E-08 | 66 | 800 | 934 | 32413 |
| KROX | <1.00E-09 | 3.000E-09 | 9.000E-09 | 64 | 802 | 936 | 32411 |
| AHRHIF | 6.000E-09 | 1.100E-07 | 1.210E-06 | 58 | 808 | 942 | 32405 |
| MZF1 | 3.400E-08 | 6.150E-07 | 7.385E-06 | 56 | 810 | 944 | 32403 |
| MAZR | 2.220E-06 | 3.442E-05 | 4.818E-04 | 51 | 815 | 949 | 32398 |
| HES1 | 2.220E-06 | 3.442E-05 | 4.818E-04 | 51 | 815 | 949 | 32398 |
| SPZ1 | 4.816E-06 | 6.967E-05 | 1.045E-03 | 50 | 816 | 950 | 32397 |
| EGR1 | 1.023E-05 | 1.306E-04 | 2.219E-03 | 49 | 817 | 951 | 32396 |
| MTF1 | 1.023E-05 | 1.306E-04 | 2.219E-03 | 49 | 817 | 951 | 32396 |
| EGR2 | 2.126E-05 | 2.428E-04 | 4.613E-03 | 48 | 818 | 952 | 32395 |
| ZIC1 | 2.126E-05 | 2.428E-04 | 4.613E-03 | 48 | 818 | 952 | 32395 |
| ZIC2 | 4.324E-05 | 4.691E-04 | 9.382E-03 | 47 | 819 | 953 | 32394 |
| AHR | 8.601E-05 | 8.483E-04 | 1.866E-02 | 46 | 820 | 954 | 32393 |
| USF | 8.601E-05 | 8.483E-04 | 1.866E-02 | 46 | 820 | 954 | 32393 |
| CACCCBF | 1.673E-04 | 1.578E-03 | 3.630E-02 | 45 | 821 | 955 | 32392 |
| HIF1 | 3.181E-04 | 2.761E-03 | 6.902E-02 | 44 | 822 | 956 | 32391 |
| SMAD4 | 3.181E-04 | 2.761E-03 | 6.902E-02 | 44 | 822 | 956 | 32391 |
| PAX3 | 1.072E-03 | 8.310E-03 | 2.327E-01 | 42 | 824 | 958 | 32389 |
| NRF1 | 1.072E-03 | 8.310E-03 | 2.327E-01 | 42 | 824 | 958 | 32389 |
| AP2a | 1.072E-03 | 8.310E-03 | 2.327E-01 | 42 | 824 | 958 | 32389 |
| USF | 1.900E-03 | 1.422E-02 | 4.123E-01 | 41 | 825 | 959 | 32388 |
The web based application Transfind was used to predict common transcription factor binding sites among the lists of upregulated and downregulated host genes. Predictions of mouse transcription factor binding sites were made with promoter sets of 1000nt from 800nt upstream to 200nt downstream and compared with 1000 genes with the highest predicted factor affinities among 33,837 total mouse genes. Possible factors were represented by the TRANSFAC matrix.