Table 1

Differential expression of OCT4 and NANOG targets in RNAi experiments

Method for determining bound targets

Percent of differentially expressed OCT4 targets on OCT4 knockdown

Percent of differentially expressed NANOG targets on NANOG knockdown

ChIP-chip only

33.9% (390/1,151)

21.4% (192/898)

ChIP-PET only

29% (114/393)

14.8% (91/616)

ChIP-chip + ChIP-PET

70.3% (83/118)

33.5% (73/218)

Percent of regulated genes

Upregulated

39.4%

50.6%

Downregulated

60.6%

49.4%

Mathur et al. Genome Biology 2008 9:R126   doi:10.1186/gb-2008-9-8-r126