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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.