Table 2

Association of adjacent genes in terms of number of TFs that bind/regulate both genes

#pair

Co-expression

Functional association




#TF

H2h

H2t

T2t

H2h

H2t

T2t

H2h

H2t

T2t


TFs with binding evidence to both genes

0 TF

405

1,761

1,229

0.229

0.221

0.245

1.839

1.641

1.690

1 TF

301

595

240

0.256

0.215

0.246

1.736

1.727

1.638

2 TFs

271

246

105

0.246

0.229

0.268

1.779

1.724

1.724

3 TFs

158

113

-

0.261

0.252

-

1.663

1.753

-

4 TFs

117

141

-

0.268

0.279

-

1.560

1.971

-

5 TFs

252

-

-

0.276

-

-

1.863

-

-

PCC

0.911

0.918

0.899

-0.247

0.877

0.396

TFs with regulation evidence to both genes

0 TF

1,053

2,098

1,212

0.232

0.212

0.237

1.673

1.572

1.644

1 TF

299

522

265

0.260

0.226

0.269

1.885

1.854

1.660

2 TFs

152

236

97

0.329

0.299

0.287

2.021

2.027

2.148

PCC

0.972

0.931

0.986

0.992

0.991

0.880

Overall

1,504

2,856

1,574


Values highlighted with bold font indicate using more than and equal to the number of TFs for sufficient pairs. For example, number of h2h pairs with four TFs with binding evidence is 117; while number of h2t pair with ≥4 TFs with binding evidence is 141. Higher co-expression or functional association indicates better gene association; see the Methods section for the details.

Chang et al. BMC Genomics 2012 13(Suppl 1):S11   doi:10.1186/1471-2164-13-S1-S11

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