Table 5.
Enrichment of different LTR elements1 in vlincRNA promoters
| K562 | HepG2 | H1-Esc | ||||||
|---|---|---|---|---|---|---|---|---|
| Repeat | # repeats2 | Fold4 (p-value) | Repeat | # repeats2 | Fold4 (p-value) | Repeat | # repeats2 | Fold4 (p-value) |
| Both Strands3 | ||||||||
| LTR12C | 30 | 9.48 (1.1E-20) | MER61-int | 4 | 22.62 (2.5E-05) | HERVH-int | 46 | 9.49 (7.9E-30) |
| LTR1 | 8 | 8.23 (4.6E-06) | Harlequin-int | 4 | 9.37 (8.8E-04) | LTR7 | 46 | 21.66 (1.42E-46) |
| THE1A | 7 | 10.49 (3.2E-06) | ||||||
| Sense Strand | ||||||||
| LTR12C | 15 | 7.48 (2.4E-09) | MER61-int | 4 | 39.50 (3.7E-06) | HERVH-int | 20 | 5.98 (3.4E-09) |
| LTR1 | 7 | 12.71 (1.2E-06) | Harlequin-int | 4 | 14.96 (2.1E-04) | LTR7 | 20 | 14.02 (5.4E-17) |
| THE1A | 6 | 16.61 (1.4E-06) | HERVE_a-int | 2 | 48.54 (9.2E-04) | |||
1Out of 505 different types of LTR elements listed in RepeatMasker
2Number of the collapsed retroviral elements (see Materials and Methods) in promoters of vlincRNAs
3Non-strand specific analysis. Repeats in both sense and antisense direction relative to the strand of the associated vlincRNAs were counted.
4Fold enrichment of what would be expected by random and the corresponding p-value. Elements with the minimum p-value of 10-4, are given in the ranking order. To obtain p-value after Bonferroni correction multiple by 505 in non-strand specific analysis or 201 in the sense strand analysis.