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Table 5 Summary of expression fold change of predicted targets in the RAi data

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

Cluster Feature Cofactor FC_RAi N b N e P c 1Q Median 3Q
UH E2f1.M00233_MEF2_04 Mef2a N 198 191 0.90 1.67 2.28 4.64
UH Sox2.M00974_SMAD_Q6_01 Smad2 H 92 90 0.89 1.82 3.01 8.50
UH Sox2.M00974_SMAD_Q6_01 Smad4 H 92 90 0.89 1.82 3.01 8.50
UH Esrrb.M00971_ETS_Q6 Elf2 H 150 144 0.92 1.62 2.32 4.12
UH Esrrb.M00971_ETS_Q6 Gabpa H 150 144 0.92 1.62 2.32 4.12
Oct4 Smad1.STAT3.M00052_NFKB Rela H 39 29 0.72 0.99 1.97 2.65
Oct4 Smad1.STAT3.M00415_ AREB6_04 Zeb1 N 36 25 0.76 1.16 1.83 2.65
Oct4 Tcfcp2l1.M00771_ETS_Q4 Elf2 H 90 82 0.82 1.16 1.97 4.15
Oct4 STAT3.M00251_XBP1_01 Xbp1 H 23 23 0.78 1.16 1.75 3.86
Oct4 Nanog.M00462_GATA6_01 Gata6 N 51 48 0.83 1.29 2.10 4.20
Oct4 Esrrb.N00007_SoxOctComp Sox2 & Oct4 P 108 101 0.82 1.14 1.95 4.04
Oct4 Oct4.M00801_CREB_Q3 Atf1 P 45 40 0.75 1.00 1.91 4.41
Myc M00233_MEF2_04 Mef2a N 170 163 0.90 1.33 1.66 2.53
Myc M00971_ETS_Q6 Gabpa H 173 167 0.89 1.33 1.70 2.67
Myc M00971_ETS_Q6 Elf2 H 173 167 0.89 1.33 1.70 2.67
Myc N00003_Otx2 Otx2 P 166 160 0.90 1.34 1.67 2.59
Myc M00034_P53_01 Trp53 P 166 160 0.91 1.34 1.67 2.71
Myc M00512_PPARG_01 Pparg N 167 160 0.89 1.34 1.70 2.59
Myc N00009_Klf4 Klf2 P 184 177 0.89 1.33 1.68 2.58
Myc N00009_Klf4 Klf5 P 184 177 0.89 1.33 1.68 2.58
Myc M00422_FOX J2_01 Foxj2 N 168 161 0.90 1.34 1.70 2.58
Myc M00724_HNF3ALPHA_Q6 Foxa1 N 177 170 0.89 1.32 1.67 2.46
Myc M01011_HNF1_Q6_01 Hnf1b N 180 174 0.89 1.34 1.67 2.48
Myc Myc.M00480_LUN101 Topors H 73 69 0.81 1.15 1.60 2.26
Myc Mycn.M00931_SP1Q6_01 Sp1 H 80 78 0.73 0.95 1.43 2.16
Myc Mycn.N00017_hB_Sall4 Sall4 P 87 82 0.74 0.98 1.57 2.60
Oct4-M M01111_RBPJK_Q4 Rbpj P 62 57 0.61 0.70 1.27 2.23
Oct4-M M00450_ZIC3_01 Zic3 P 43 41 0.63 0.80 1.28 2.23
Oct4-M N00001_Sox2 Sox2 P 49 46 0.57 0.70 1.09 1.45
Oct4-M M00225_STAT3_01 Stat3 H 44 43 0.67 0.84 1.28 1.79
  1. Note: FC_RAi is fold change of cofactor expression. Nb is the number of predicted targets for a feature. N e is the number of targets having expression available in [9]. P c is the proportion of N e genes with expected expression change. 1Q, Median, and 3Q are, respectively, the 1st quartile, the median, and the 3rd quartile of targets' fold change, which is inverted for ES-down features for convenient comparison.