Table 3.
Comparison of gene lists between HNF4α expression data, ChIP-chip data, and computational prediction of target promoters
| Gene sets in ChIP-chip experiment | HNF4 targets identified by PWM V$HNF4_Q6_1 (cut-off = 0.9) | HNF4 targets identified by local + global context | ||
| Positive* | Negative† | |||
| Gupta et al. [44] Up + Dn (133) |
13 (9.8%) | ND | 66 (49.6%) | 41 (30.8%) |
| Naiki et al. [7] Up + Dn (75)‡ |
17 (22.7%) | 32 (42.7%) | 15 (20%) | 14 (18.7%) |
| Lucas et al. [9] Up + Dn (70)‡ |
13 (18.6%) | 39 (55.7%) | 17 (24.3%) | 13 (18.6%) |
| Lucas et al. [9] NC (150)‡ |
20 (13.3%) | 99 (66%) | 29 (19.3%) | 4 (2.7%) |
*The number of differentially expressed genes with HNF4α binding sites as identified by ChIP-chip experiments. †The number of differentially expressed genes with no HNF4α binding as determined by ChIP-chip experiments. ‡The number of genes whose expression was upregulated or downregulated by more than two-fold. NC, genes with no change of expression; ND, not determined.