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Table 5 Motif Enrichment in Genes bound by Oct4 or cMyc TF Groups

From: Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells

   Oct4 Group cMyc Group
Motif Binding TF No. of genes ratio p-value No. of genes ratio p-value
SoxOct (Oct4, Sox2) 66 3.41 2.0E-21 103 0.45 6.4E-24
Oct4 (Oct4) 37 2.33 9.9E-08 151 0.81 2.5E-03
Sox2 (Sox2) 51 3.06 3.8E-15 178 0.86 1.4E-02
Nanog (Nanog) 18 2.20 5.0E-04 122 1.35 3.9E-04
Stat1 (Stat3) 34 2.83 7.3E-09 145 1.32 1.0E-04
Ebox (cMyc) 6 0.59 9.5E-01 373 4.02 2.6E-207
E2f1 (E2f1) 1 1.44 9.4E-02 284 2.25 1.2E-40
Klf4 (Klf4) 38 1.02 4.0E-01 235 0.61 1.4E-19
Lrh1 (Lrh1) 28 2.22 1.4E-05 158 1.12 6.9E-02
Elk1 (Elk1) 10 0.19 3.1E-02 170 1.64 8.6E-11
  1. Sequences co-bound by all TFs of the Oct4 group (Oct4, Sox2, Nanog, Smad1, and Stat3) or all TFs of the cMyc group (cMyc, nMyc, E2f1, and Zfx) in the Chen et al data set were scanned for relevant motifs, plus the Lrh1 (Nr5a2) and Elk1 motifs. There were 122 genes bound by all TFs in the Oct4 group and 1173 genes bound by all TFs in the cMyc group. Enrichments, computed by comparing against motif scans in control sequences, and p-values are shown below.