Table 1 Differential expression analysis between control and LOXL2 knockdown of repetitive elements
From: LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells
Locus | Ctrl_mean | Loxl2_mean | Prob | log2FC |
---|---|---|---|---|
Alu | 3,601,718.96 | 3,714,313.36 | 1.00 | 0.04 |
RNA | 2,918,334.55 | 3,045,475.41 | 0.99 | 0.06 |
L1 | 2,837,069.25 | 2,730,921.52 | 0.97 | −0.06 |
ERV1 | 370,405.10 | 353,869.12 | 0.95 | −0.07 |
TcMar-Tigger | 239,662.63 | 252,421.97 | 0.87 | 0.07 |
UCON19 | 0.51 | 1.23 | 0.76 | 1.28 |
UCON18 | 0.51 | 1.23 | 0.76 | 1.28 |
hAT-Tip100 | 34,122.72 | 38,990.93 | 0.76 | 0.19 |
ERVK | 8,958,641.10 | 9,448,789.20 | 0.76 | 0.08 |
MIR | 673,530.34 | 692,895.61 | 0.76 | 0.04 |
hAT | 12,908.30 | 16,757.15 | 0.76 | 0.38 |
TcMar-Mariner | 33,897.47 | 38,475.09 | 0.75 | 0.18 |
UCON4 | 234.62 | 360.51 | 0.74 | 0.62 |
hAT-Charlie | 374,265.61 | 380,188.93 | 0.72 | 0.02 |
UCON16 | 6.58 | 10.85 | 0.72 | 0.72 |
Penelope | 7.08 | 11.83 | 0.70 | 0.74 |
ERVL-MaLR | 399,009.16 | 406,080.51 | 0.70 | 0.03 |
UCON31 | 61.20 | 87.49 | 0.70 | 0.52 |
MER130 | 15.18 | 21.75 | 0.69 | 0.52 |
UCON2 | 320.19 | 434.63 | 0.69 | 0.44 |
UCON10 | 7.09 | 10.93 | 0.67 | 0.63 |
UCON28c | 10.12 | 14.81 | 0.63 | 0.55 |
Eulor4 | 1.26 | 1.98 | 0.55 | 0.65 |
UCON12 | 14.14 | 4.94 | 0.52 | −1.52 |
TcMar-Tc2 | 12,524.35 | 13,658.11 | 0.51 | 0.13 |
UCON24 | 1.27 | 0.49 | 0.47 | −1.36 |
UCON17 | 3.03 | 1.23 | 0.46 | −1.30 |
ERVL | 174,857.94 | 177,852.71 | 0.44 | 0.02 |
MamRep605 | 7848.87 | 8610.92 | 0.41 | 0.13 |
UCON28a | 201.88 | 253.61 | 0.39 | 0.33 |
Satellite | 28,748.18 | 25,760.18 | 0.37 | −0.16 |
UCON26 | 532.62 | 618.38 | 0.35 | 0.22 |
SVA_B | 2696.77 | 3025.33 | 0.31 | 0.17 |
acro | 14.16 | 10.88 | 0.30 | −0.38 |
UCON11 | 6.08 | 3.93 | 0.29 | −0.63 |
UCON15 | 4.29 | 2.25 | 0.29 | −0.93 |
MuDR | 1610.89 | 1799.90 | 0.28 | 0.16 |
SVA_F | 3968.24 | 4322.50 | 0.26 | 0.12 |
Gypsy | 18,034.32 | 16,836.16 | 0.26 | −0.10 |
DNA | 5850.42 | 6284.72 | 0.25 | 0.10 |
Dong-R4 | 3696.41 | 3198.15 | 0.25 | −0.21 |
UCON9 | 18.69 | 12.78 | 0.24 | −0.55 |
Centre | 11,923.53 | 12,544.21 | 0.22 | 0.07 |
Merlin | 297.42 | 327.87 | 0.19 | 0.14 |
SVA_D | 11,475.76 | 11,978.90 | 0.19 | 0.06 |
UCON28b | 26.33 | 30.80 | 0.18 | 0.23 |
LTR | 1842.20 | 1987.87 | 0.18 | 0.11 |
UCON8 | 75.37 | 65.33 | 0.15 | −0.21 |
TcMar | 8328.59 | 8597.66 | 0.11 | 0.05 |
SVA_A | 1741.04 | 1827.45 | 0.10 | 0.07 |
CR1 | 85,288.67 | 84,328.51 | 0.09 | −0.02 |
Helitron | 5017.41 | 5157.97 | 0.06 | 0.04 |
UCON6 | 1,277.83 | 1,325.68 | 0.06 | 0.05 |
RTE | 30,497.19 | 29,901.20 | 0.06 | −0.03 |
PiggyBac | 4590.52 | 4349.34 | 0.06 | −0.08 |
UCON22 | 12.14 | 10.47 | 0.06 | −0.21 |
UCON5 | 11.14 | 9.87 | 0.06 | −0.17 |
telo | 489.07 | 507.40 | 0.05 | 0.05 |
L2 | 614,402.54 | 610,776.39 | 0.05 | −0.01 |
Deu | 2157.42 | 2220.57 | 0.05 | 0.04 |
hAT-Blackjack | 11,106.77 | 11,287.96 | 0.05 | 0.02 |
UCON1 | 3.04 | 3.25 | 0.04 | 0.10 |
UCON27 | 72.82 | 74.65 | 0.03 | 0.04 |
UCON20 | 12.13 | 10.95 | 0.02 | −0.15 |
MamRep564 | 756.04 | 712.80 | 0.02 | −0.08 |
RTE-BovB | 1064.66 | 1011.37 | 0.02 | −0.07 |
ERV | 440.91 | 422.61 | 0.01 | −0.06 |
SINE | 4912.94 | 4894.14 | 0.00 | −0.01 |
UCON25 | 2.27 | 2.20 | 0.00 | −0.04 |
SVA_E | 1087.33 | 1076.64 | 0.00 | −0.01 |