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Table 3 Comparison of gene lists between HNF4α expression data, ChIP-chip data, and computational prediction of target promoters

From: Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context

 

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%)

  1. *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.