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Table 1 Average Alu and breadth composition for human genes associated with different biological processes

From: Do Alu repeats drive the evolution of the primate transcriptome?

Biological process

Gene number

Breadth

Alu

  

Mean

SD

Mean

SD

Protein biosynthesis

255

37.2

24.11

0.2833

0.1932

Ubiquitin-dependent protein catabolism

111

35.45

23.57

0.2462

0.1707

Intracellular protein transport

207

33.45

22.93

0.2602

0.2001

Nuclear mRNA splicing, via spliceosome

163

31.56

22.56

0.3004

0.2186

Protein folding

201

31.33

22.5

0.2597

0.1716

Protein transport

193

30.72

23.46

0.2759

0.1749

Ubiquitin cycle

270

28.21

23.77

0.2683

0.1826

Protein amino acid dephosphorylation

154

26.96

20.75

0.2186

0.1792

Protein modification

104

26.53

21.2

0.2425

0.1772

Regulation of progression through cell cycle

185

26.5

22.25

0.248

0.2014

Cell cycle

186

26.32

21.2

0.2248

0.1852

Protein complex assembly

108

26.23

22.33

0.2513

0.1806

Cell motility

105

26.1

20.57

0.2217

0.1976

Transcription

101

26.01

23.31

0.2417

0.1906

Electron transport

317

25.87

22.7

0.198

0.1703

Negative regulation of cell proliferation

122

25.57

22.99

0.205

0.1657

Small GTPase mediated signal transduction

194

25.47

21.47

0.2251

0.1775

Intracellular signaling cascade

406

25.1

21.65

0.2108

0.1811

Metabolism

440

24.68

20.43

0.1916

0.1681

Carbohydrate metabolism

191

24.48

21.51

0.2164

0.1956

Apoptosis

260

24.03

20.43

0.218

0.1906

Cytokinesis

111

23.94

21.26

0.2082

0.1773

Regulation of transcription from RNA polymerase II promoter

150

23.59

21.86

0.2332

0.1938

DNA repair

132

23.58

21.06

0.2478

0.179

Cell proliferation

223

23.26

20.79

0.1974

0.1847

Protein amino acid phosphorylation

611

23.21

20.35

0.2391

0.1881

Protein ubiquitination

346

22.39

21.55

0.2305

0.1772

Transport

580

22.07

20.49

0.2184

0.1862

Transcription from RNA polymerase II promoter

171

21.85

22.01

0.2131

0.192

Signal transduction

896

21.81

20.21

0.1882

0.1702

Lipid metabolism

156

21.24

20.66

0.1978

0.1732

Cell surface receptor linked signal transduction

126

21.16

20.82

0.1821

0.1603

DNA replication

103

21.08

21.71

0.2377

0.1818

Immune response

266

20.72

18.79

0.1748

0.1743

Cell adhesion

439

20.23

18.16

0.1377

0.1425

Inflammatory response

174

20.22

19.76

0.1585

0.1693

Proteolysis

474

19.38

19.72

0.1984

0.1739

Nervous system development

242

19.32

19.21

0.1575

0.1769

Sensory perception of smell

132

19.21

18.16

0.1

0.1211

Regulation of transcription, DNA dependent

1681

18.42

20.2

0.2021

0.1877

Homophilic cell adhesion

117

17.56

18.49

0.1042

0.1238

Chemotaxis

105

17.15

16.11

0.1682

0.162

Development

474

17.05

18.67

0.1488

0.1737

Muscle development

127

16.9

17.06

0.1809

0.1695

Spermatogenesis

107

16.5

18.73

0.1925

0.1767

G-protein-coupled receptor protein signaling pathway

547

16.49

18.41

0.1388

0.1478

Ion transport

231

16.26

17.18

0.1437

0.1471

Synaptic transmission

190

15.84

16.34

0.1394

0.1516

Visual perception

168

15.82

19.07

0.1663

0.159

Cell-cell signaling

269

15.05

17.83

0.1546

0.1559

Phosphate transport

104

14.34

15.81

0.1395

0.1712

Potassium ion transport

168

14.27

16.54

0.1306

0.1533

Cation transport

185

13.17

17.41

0.1506

0.1541

  1. Mean and standard deviation (SD) for breadth and Alu content in the upstream region 2 to 6 kilobases away from transcription starting site are shown for genes associated to each biological process. Only Gene Ontology (GO) categories containing more than 100 genes from our sample were included in the analyses. Note that GO categories are not mutually exclusive.