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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.