Table 1

GO terms associated with TE-poor genes

Under-represented TE type


GO term

Description

Alu

L1

L2

LTR

DNA transp.

MIR


Molecular function

N

MCS

IG

N

MCS

IG

N

MCS

IG

N

MCS

IG

N

MCS

IG

N

MCS

IG


GO:0003676

Nucleic acid binding

-

-

-

-

-

-

468

0.88*

-0.44*

598

0.86*

-0.27*

-

-

-

327

1.07

-0.29*

GO:0003677

DNA binding

-

-

-

-

-

-

-

-

-

394

1.27*

-0.17

-

-

-

219

1.6*

-0.34*

GO:0003723

RNA binding

-

-

-

-

-

-

131

0.08

-0.49*

153

0.13

-0.42*

-

-

-

91

0.03

-0.12

GO:0003700

Transcription factor activity

138

2.45*

-0.63*

171

1.9*

-0.51*

160

2.1*

-0.41*

220

1.82*

-0.09

165

2.18*

-0.65*

125

2.23*

-0.76*

GO:0030528

Transcription regulator activity

159

2.35*

-0.59*

-

-

-

-

-

-

279

1.57*

-0.1

-

-

-

152

2.04*

-0.67*

GO:0004871

Signal transducer activity

348

0.32

-0.45*

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0004888

Transmembrane receptor activity

138

0.23

-0.31

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0005102

Receptor binding

137

0.5

-0.57*

170

0.29

0.03

149

0.24

0.14

192

0.33

0.2

155

0.32

-0.02

-

-

-

GO:0001664

G-protein-coupled receptor binding

-

-

-

25

-0.14

-0.23

-

-

-

-

-

-

26

-0.16

-0.1

-

-

-

GO:0008083

Growth factor activity

47

0.98

-0.16

-

-

-

-

-

-

64

0.73

0.45*

-

-

-

-

-

-

GO:0005125

Cytokine activity

69

0.59

-0.71*

84

0.29

-0.36

-

-

-

91

0.44

0.48*

76

0.42

0.24

-

-

-

GO:0008009

Chemokine activity

-

-

-

25

-0.14

-0.23

-

-

-

-

-

-

26

-0.16

-0.1

-

-

-

GO:0042379

Chemokine receptor binding

-

-

-

25

-0.14

-0.23

-

-

-

-

-

-

26

-0.16

-0.1

-

-

-

GO:0005179

Hormone activity

33

0.49

-0.71

-

-

-

41

0.11*

-0.44

-

-

-

34

0.19*

-0.47

27

0.49

-0.64

GO:0005184

Neuropeptide hormone activity

10

-0.12

0.27

-

-

-

11

0.01

0.68

-

-

-

-

-

-

-

-

-

GO:0004252

Serine-type endopeptidase activity

-

-

-

50

-0.34*

-0.01

-

-

-

-

-

-

-

-

-

-

-

-

GO:0004263

Chymotrypsin activity

-

-

-

38

-0.45*

-0.1

-

-

-

-

-

-

-

-

-

-

-

-

GO:0004295

Trypsin activity

-

-

-

39

-0.45*

-0.21

-

-

-

-

-

-

-

-

-

-

-

-

GO:0003735

Structural constituent of ribosome

-

-

-

100

-0.34*

-0.25

89

-0.41*

-0.72*

116

-0.37*

-0.58*

79

-0.35*

-0.5

63

-0.33*

-0.47

GO:0005198

Structural molecule activity

-

-

-

212

-0.04

-0.4*

192

-0.11*

-0.43*

260

-0.07

-0.2

-

-

-

-

-

-

Biological process

GO:0007275

Development

335

1.41*

-0.55*

410

1.13*

-0.45*

386

1.19*

-0.23

512

1.09*

0.1

384

1.32*

-0.45*

258

1.58*

-0.48*

GO:0009653

Morphogenesis

222

1.24*

-0.48*

-

-

-

-

-

-

334

0.94*

0.21*

-

-

-

-

-

-

GO:0009887

Organogenesis

186

1.03*

-0.46*

-

-

-

-

-

-

270

0.8*

0.22*

-

-

-

-

-

-

GO:0009888

Histogenesis

-

-

-

-

-

-

-

-

-

47

0.49

0.46

-

-

-

-

-

-

GO:0008544

Epidermis development

24

-0.27

-1.4*

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0001501

Skeletal development

36

1.4*

-0.23

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0007267

Cell-cell signaling

137

0.71*

-0.27

162

0.69*

0.03

-

-

-

-

-

-

-

-

-

-

-

-

GO:0007166

Cell surface receptor linked signal transduction

161

0.29*

-0.45*

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0007186

G-protein coupled receptor protein signaling pathway

93

0.17

-0.51*

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0006952

Defense response

172

0.13*

-0.75*

217

-0.08*

-0.16

202

-0.11*

-0.19

259

0*

0.01

219

-0.04*

-0.2

-

-

-

GO:0006955

Immune response

155

0.17*

-0.7*

201

-0.08*

-0.19

-

-

-

-

-

-

202

-0.05*

-0.17

-

-

-

GO:0050896

Response to stimulus

268

0.13

-0.61*

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0009607

Response to biotic stimulus

187

0.1*

-0.69*

240

-0.1*

-0.21

222

-0.14*

-0.16

290

-0.05*

0

235

-0.07*

-0.25

-

-

-

GO:0009613

Response to pest, pathogen or parasite

99

-0.02*

-0.8*

-

-

-

-

-

-

-

-

-

127

-0.33*

-0.13

-

-

-

GO:0043207

Response to external biotic stimulus

106

-0.09*

-0.86*

-

-

-

-

-

-

-

-

-

134

-0.36*

-0.17

-

-

-

GO:0006817

Phosphate transport

27

-0.05

-0.39

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0006820

Anion transport

41

0.03

-0.47

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0015698

Inorganic anion transport

38

0.03

-0.49

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0006350

Transcription

-

-

-

-

-

-

-

-

-

386

1.22*

-0.16

-

-

-

211

1.43*

-0.43*

GO:0045449

Regulation of transcription

-

-

-

-

-

-

-

-

-

365

1.31*

-0.15

-

-

-

198

1.53*

-0.45*

GO:0006351

Transcription, DNA-dependent

-

-

-

-

-

-

-

-

-

369

1.25*

-0.16

-

-

-

203

1.48*

-0.45*

GO:0006355

Regulation of transcription, DNA-dependent

-

-

-

-

-

-

267

1.38*

-0.23

355

1.31*

-0.16

-

-

-

196

1.53*

-0.46*

GO:0006139

Nucleobase, nucleoside, nucleotide and nucleic acid metabolism

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

301

1.08

-0.23

GO:0019219

Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism

-

-

-

-

-

-

-

-

-

371

1.29*

-0.16

-

-

-

202

1.51*

-0.46*

GO:0019222

Regulation of metabolism

-

-

-

-

-

-

303

1.32*

-0.2

409

1.24*

-0.16

-

-

-

217

1.54*

-0.38*

GO:0006412

Protein biosynthesis

-

-

-

144

-0.14

-0.34

-

-

-

179

-0.1*

-0.48*

-

-

-

-

-

-

GO:0050876

Reproductive physiological process

18

1.19

-0.76

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

GO:0000003

Reproduction

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

44

0.09*

-0.38

GO:0019953

Sexual reproduction

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

43

0.06*

-0.38

GO:0007276

Gametogenesis

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

39

0.14*

-0.39

GO:0048232

Male gamete generation

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

33

0.07*

-0.05

GO:0007283

Spermatogenesis

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

33

0.07*

-0.05


Significant differences are marked with an asterisk. DNA transp., DNA transposon; N, number of contributing genes; MCS, fractional intronic MCS density deviation (see text); IG, fractional igTEna deviation (see text).

Sironi et al. Genome Biology 2006 7:R120   doi:10.1186/gb-2006-7-12-r120

Open Data