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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.
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BMC Genomics

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