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Table 1 Transcription Factor Binding in Ivanova et al Networks

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

Unsigned Network

Module

No. of genes

Oct4Complex

cMycComplex

Suz12

blue

899

0.863, 0.232

1.09, 0.0398

0.956, 0.366

brown

1241

0.862, 0.179

0.757, 3.09e-09

1.92, 2.5e-21

green

1556

0.825, 0.0832

0.811, 1.78e-07

1.13, 0.0496

grey

7407

1.16, 2.37e-05

1.18, 4.62e-45

0.866, 2.17e-07

red

1673

1.1, 0.169

1.68, 6.75e-74

0.281, 7.61e-28

turquoise

5721

0.898, 0.0268

0.801, 4.3e-36

1.2, 6.96e-10

yellow

1053

1.14, 0.15

1.46, 5.74e-22

0.458, 7.39e-10

Signed Network

black

941

2.9, 7.25e-24

1.83, 4.8e-58

0.288, 1.95e-15

blue

220

0.608, 0.165

0.488, 1.59e-07

1.93, 4.42e-05

brown

1090

0.736, 0.0402

0.754, 2.04e-08

1.99, 3.27e-21

cyan

581

0.783, 0.174

0.931, 0.15

1.78, 2.58e-08

green

1538

0.731, 0.0138

0.778, 1.14e-09

1.12, 0.0534

grey

4428

0.949, 0.224

0.853, 2.38e-14

1.13, 0.000604

magenta

514

1.09, 0.286

1.11, 0.0548

0.824, 0.122

midnightblue

649

1.61, 0.00131

1.89, 2.87e-45

0.181, 6.99e-15

pink

2242

1.4, 4.41e-05

1.85, 8.63e-160

0.341, 3.32e-31

red

1270

1.01, 0.429

1.56, 1.19e-37

0.371, 8.07e-16

salmon

650

1.03, 0.388

1.19, 0.00083

0.67, 0.00378

tan

445

2.16, 4.62e-06

1.71, 4.65e-21

0.37, 3.14e-06

turquoise

5205

0.679, 2.41e-09

0.749, 3.51e-49

1.24, 2.71e-11

yellow

1042

1.05, 0.326

1.35, 1.9e-13

0.633, 4.69e-05

  1. Enrichment for binding by the Oct4 and cMyc TF Groups and Suz12.
  2. Each enrichment score (before the comma) is followed by its corresponding p-value (after the comma) calculated from the hyper-geometric distribution. P-values are uncorrected for multiple comparisons.
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