Table 2. Criteria table for transcription response element inclusion in gene regulatory network models.
| TRE | p-value | Evolutionary conservation factor | Frequency ratio |
|---|---|---|---|
| Promoter | |||
| E2F-1/V$E2F1_Q3_01 |
0.00095 |
2 |
3.725 |
| Oct-1/V$OCT1_02 |
0.00801 |
3 |
4.25 |
| Nkx2–5/V$NKX25_02 |
0.05404 |
2 |
2.3 |
| Poly A/V$LDSPOLYA_B |
0.07291 |
2 |
2.16 |
| IRF/V$IRF_Q6_01 |
0.08969 |
2 |
2.33 |
| COMP1/V$COMP1_01 |
0.03569 |
2 |
2.52 |
| First intron | |||
| Evi-1/V$EVI1_05 |
0.00003 |
2 |
13.86 |
| Oct-1/V$OCT1_02 |
0.00043 |
2 |
6.32 |
| GR/V$GRE_C |
0.00045 |
2 |
14.6 |
| SMAD-3/V$SMAD3_Q6 |
0.00071 |
3 |
3.18 |
| HNF-1/V$HNF1_01 |
0.00918 |
2 |
7.35 |
| AP-1/V$AP1_C | 0.01893 | 2 | 4.87 |
Represented for each transcription response elements (TRE) identified in the promoter and intron regions of each gene are the TRANSFAC identifier name, the p-value, the evolutionary conservation factor (ECF), and the frequency ratio (FR) as defined in Methods. TREs included in this table are those with p-value <0.1, ECF=2, and FR>3. The full table of values for all TREs analyzed is contained in Appendix 30 (promoters) and Appendix 31 (introns).