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