Table 2.
CpG hypo-methylation in tissue-specific lncRNA promoters
| Tissue | Mutual enrichment between GC content and tissue-specificity |
Mutual enrichment between hypo-methylation and tissue-specificity |
|
|---|---|---|---|
| Normal/subnormal cells | Cancer cells | ||
| Thyroid |
3.89e-31 |
No methylation data |
No methylation data |
| Prostate |
5.76e-22 |
4.16e-11 (PrEC) |
0.002 (LNCaP) |
| Adrenal |
5.46e-20 |
No methylation data |
No methylation data |
| Brain |
1.57e-14 |
1.21e-8 (NH-A) |
5.55e-5 (U87) |
| Ovary |
8.80e-12 |
No methylation data |
0.0085 (ovcar-3) |
| Lymph node |
3.64e-6 |
No methylation data |
No methylation data |
| Adipose |
9.25e-6 |
No methylation data |
No methylation data |
| Foreskin |
2.25e-5 |
0.72 (BJ) |
No methylation data |
| Breast |
4.40e-5 |
5.08e-5 (HMEC) |
8.45e-5 (MCF7) |
| 2.0e-10 (MCF10A) |
0.0065 (T-47D) |
||
| Kidney |
6.34e-5 |
1.56e-5 (HEK293) |
No methylation data |
| White blood cell |
3.78e-4 |
0.6 (GM12878) |
0.21 (Jurkat) |
| Placenta |
0.011 |
No methylation data |
No methylation data |
| Colon |
0.012 |
No methylation data |
1.0 (Caco-2) |
| Skeletal muscle |
0.04 |
0.34 (SKMC) |
No methylation data |
| Lung |
0.33 |
No methylation data |
No methylation data |
| Heart |
1.0 |
1.0 (HCM) |
No methylation data |
| 1.0 (HCF) | |||
| Liver |
1.0 |
1.0 (Hepatocytes) |
1.0 (HepG2) |
| Testes |
1.0 |
No methylation data |
1.0 (NT2-D1) |
| Lung fibroblasts |
1.0 |
1.0 (IMR90) |
No methylation data |
| 1.0 (AGO4450) | |||
We calculated the mutual enrichment between DNA hypo-methylation and tissue specificity for the lncRNA promoters. CpG methylation data was taken from UCSC Table Browser [39] (ENCODE/HAIB).