Skip to main content

Table 4 Summary of selected features

From: Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells

Cluster ES U/D Feature Locuslink Cofactor FC Role P-value LS
UH U E2f1.M00233_MEF2_04 17258 Mef2a N DR 8.66E-07  
UH U Sox2.M00974_SMAD _Q6_01 17126 Smad2 N DR 1.03E-04  
UH U Sox2.M00974_SMAD_ Q6_01 17128 Smad4 H EA/DR 1.03E-04 [38]
UH U Esrrb.M00971_ETS_Q6 13709 Elf1 N DR 1.25E-04  
UH U Esrrb.M00971_ETS_Q6 69257 Elf2 N DR 1.25E-04  
UH U Esrrb.M00971_ETS_Q6 14390 Gabpa P EA 1.25E-04  
Oct4 D Smad1.STAT3.M00052_NFKB 19697 Rela N DA 2.66E-07 [19]
Oct4 D Smad1.STAT3.M00415_AREB6_04 21417 Zeb1 N DA 1.51E-06 [20]
Oct4 U Tcfcp2l1.M00771_ETS_Q4 69257 Elf2 N DR 1.82E-06  
Oct4 U Tcfcp2l1.M00771_ETS_Q4 13709 Elf1 N DR 1.82E-06  
Oct4 U STAT3.M00251_XBP1_01 22433 Xbp1 N DR 1.37E-05  
Oct4 U Nanog.M00462_GATA6_01 14465 Gata6 N DR 2.69E-05 [21]
Oct4 U Nanog.M00134_HNF4_01 15378 Hnf4a N DR 1.05E-04  
Oct4 U Esrrb.N00007_SoxOctComp 18999 Sox2 & Oct4 P EA 1.32E-04  
Oct4 U Oct4.M00801_CREB_Q3 11911 Atf2 H EA/DR 1.66E-04  
Oct4 U Oct4.M00801_CREB_Q3 11908 Atf1 H EA/DR 1.66E-04  
Oct4 U Oct4.M00801_CREB_Q3 11910 Atf7 N DR 1.66E-04  
Myc D M00233_MEF2_04 17258 Mef2a N DA 3.83E-05  
Myc D M00971_ETS_Q6 14390 Gabpa P ER 4.92E-05  
Myc D M00971_ETS_Q6 69257 Elf2 N DA 4.92E-05  
Myc D M00971_ETS_Q6 13709 Elf1 N DA 4.92E-05  
Myc D N00003_Otx2 18424 Otx2 P ER 1.05E-04 [22, 23]
Myc D M00034_P53_01 22059 Trp53 P ER 1.61E-04 [24]
Myc D M00421_MEIS1BHOXA9_02 17268 Meis1 N DA 1.95E-04  
Myc D M00512_PPARG_01 19016 Pparg N DA 3.64E-04 [25]
Myc D N00009_Klf4 16600 Klf4 N DA 3.97E-04 [26]
Myc D N00009_Klf4 16598 Klf2 P ER 3.97E-04 [26]
Myc D N00009_Klf4 12224 Klf5 H ER/DA 3.97E-04 [26]
Myc D M00764_HNF4_DR1_Q3 15378 Hnf4a N DA 8.46E-04  
Myc D M00422_FOXJ2_01 60611 Foxj2 N DA 9.43E-04  
Myc D M00724_HNF3ALPHA_Q6 15375 Foxa1 N DA 9.81E-04  
Myc D M01011_HNF1_Q6_01 21410 Hnf1b N DA 1.16E-03  
Myc U Myc.M00480_LUN1_01 106021 Topors H EA/DR 1.43E-04  
Myc U Mycn.M00931_SP1_Q6_01 20683 Sp1 H EA/DR 1.69E-04  
Myc U Mycn.N00017_hB_Sall4 99377 Sall4 H EA/DR 1.81E-04 [39]
Oct4-M U M01111_RBPJK_Q4 19664 Rbpj P EA 6.51E-06 [28, 29]
Oct4-M U M00450_ZIC3_01 22773 Zic3 P EA 1.74E-05 [30]
Oct4-M U N00001_Sox2 20674 Sox2 P EA 2.45E-04 [3]
Oct4-M U M00225_STAT3_01 20848 Stat3 N DR 2.50E-04 [6]
  1. Note: UH cluster is shorthand for the uniformly-high cluster; Oct4-M cluster is shorthand for the Oct4-moderate cluster. The column "ES U/D" indicates whether a feature is an ES-up feature (U) or an ES-down feature (D). Locuslinks, cofactor gene names, and fold change (FC) of gene expression (N--negative fold change, P--positive fold change, H--uniformly high) of cofactors are listed correspondingly. The column "LS" indicates related literature support for a feature.