Skip to main content

Table 2 Gene number (proportion) among differentially expressed genes according to the TE-content category and their enrichment in histone modifications in cancer condition

From: The transposable element environment of human genes is associated with histone and expression changes in cancer

TE category

Total genome

Down-regulated genes

Up-regulated genes

depleted in H3K4me1

depleted in H3K4me3

depleted in H3K79me2

enriched in H3K27me3

enriched in H3K4me1

enriched in H3K4me2

enriched in H3K4me3

enriched in H3K79me2

SINE-rich

2119 (11.11 %)

156 (9.46 %)

146 (10.28 %)

161 (9.12 %)

114 (7.53 %)

298 (12.77 %)

292 (12.45 %)

310 (12.00 %)

227 (12.48 %)

LINE-rich

972 (5.10 %)

88 (5.34 %)

82 (5.77 %)

94 (5.32 %)

80 (5.28 %)

96 (4.11 %)

107 (4.56 %)

111 (4.30 %)

78 (4.29 %)

DNA-rich

824 (4.32 %)

91 (5.52 %)

74 (5.21 %)

87 (4.93 %)

73 (4.82 %)

96 (4.11 %)

101 (4.31 %)

97 (3.76 %)

77 (4.23 %)

LTR-rich

1800 (9.44 %)

255 (15.46 %)

204 (14.37 %)

284 (16.08 %)

272 (17.97 %)

247 (11.58 %)

238 (10.15 %)

267 (10.34 %)

209 (11.49 %)

SINE-intermediate

1784 (9.35 %)

118 (7.16 %)

111 (7.82 %)

98 (5.55 %)

73 (4.82 %)

229 (9.81 %)

236 (10.06 %)

250 (9.68 %)

177 (9.73 %)

LINE-intermediate

20 (0.10 %)

0 (0.00 %)

1 (0.07 %)

1 (0.06 %)

2 (0.13 %)

1 (0.04 %)

1 (0.04 %)

0 (0.00 %)

1 (0.05 %)

DNA-intermediate

15 (0.08 %)

1 (0.06 %)

2 (0.14 %)

1 (0.06 %)

2 (0.13 %)

3 (0.13 %)

4 (0.17 %)

2 (0.08 %)

3 (0.16 %)

LTR-intermediate

63 (0.33 %)

7 (0.42 %)

5 (0.35 %)

6 (0.34 %)

1 (0.07 %)

4 (0.17 %)

5 (0.21 %)

3 (0.12 %)

3 (0.16 %)

TE-free

4300 (22.55 %)

240 (14.55 %)

221 (15.56 %)

227 (12.85 %)

170 (11.23 %)

404 (17.31 %)

407 (17.36 %)

454 (17.58 %)

314 (17.26 %)

All-TE-intermediate

191 (1.67 %)

14 (0.85 %)

6 (0.42 %)

20 (1.13 %)

16 (2.77 %)

41 (1.76 %)

40 (1.71 %)

44 (1.70 %)

37 (2.03 %)

All-TE-rich

318 (1.00 %)

27 (1.64 %)

35 (2.46 %)

42 (2.38 %)

42 (1.06 %)

25 (1.07 %)

30 (1.28 %)

32 (1.24 %)

18 (0.99 %)

Mix

6665 (34.95 %)

652 (39.54 %)

533 (37.53 %)

745 (42.19 %)

669 (44.19 %)

890 (38.13 %)

884 (37.70 %)

1013 (39.22 %)

675 (37.11 %)

P values Chi2 homogeneity tests

 

<2.2e-16

6.863e-14

<2.2e-16

<2.2e-16

<2.2e-16

2.208e-06

3.434e-09

5.405e-06

Total gene number

19071

1649

1420

1766

1514

2334

2345

2583

1819

  1. Chi2 homogeneity tests to compare the gene number for each modification to the gene number in total genome p < 6.25e-3