Table 2. Transcription factor-binding sites associated with C/EBPβ sites bound in vivo.
| Binding sites | Maximum total length, bp | Frequency in C/EBP targets (n = 15), % | Frequency in microarray set (n = 2,122), % | P value (corrected) |
|---|---|---|---|---|
| C/EBPβ, DBP | 342 | 80 | 16 | 4.0 × 10-4 |
| C/EBPβ, ISRE | 608 | 80 | 14 | 7.7 × 10-5 |
| C/EBPβ, PPAR-DR1 | 736 | 73 | 19 | 0.04 |
| C/EBPβ, DBP, ISRE | 790 | 80 | 6.4 | 1.9 × 10-6 |
| C/EBPβ, DBP, PPAR-DR1 | 963 | 80 | 12 | 3.5 × 10-3 |
| C/EBPβ, ISRE, PPAR-DR1 | 663 | 80 | 9.3 | 1.9 × 10-4 |
| C/EBPβ, DBP, ISRE, PPAR-DR1 | 768 | 80 | 4.2 | 2.7 × 10-6 |
Potential C/EBPβ DNA-binding partners were evaluated as described in Materials and Methods. For each combination, the maximum distance between the outermost sites is given, and the frequency of positive genes in the 15 ChIP-positive targets and in the entire set of genes present on the mouse promoter microarray. The sites may be in any order or orientation. The P value is corrected for multiple testing. The LOD scores for each site are as follows: C/EBPβ, 8.9; D-site-binding protein (DBP), 9.2; ISRE, 9.0; PPAR-DR1, 9.0 for the pair with C/EBPβ and 8.1 for the higher order combinations. The transfac v. 7.3 position-sensitive scoring matrices used are as follows: M00109/C/EBPB_01, M00624/DBP_Q6, M00258/ISRE_01, and M00763/PPAR_DR1_01.