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Table 5 Enrichment of different LTR elements1 in vlincRNA promoters

From: VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer

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)

   
  1. 1Out of 505 different types of LTR elements listed in RepeatMasker
  2. 2Number of the collapsed retroviral elements (see Materials and Methods) in promoters of vlincRNAs
  3. 3Non-strand specific analysis. Repeats in both sense and antisense direction relative to the strand of the associated vlincRNAs were counted.
  4. 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.
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Genome Biology

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