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Table 1 GO terms associated with TE-poor genes

From: Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns

   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
  1. 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).
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Genome Biology

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