Table 1.
Number of active genes annotated as bi- or unidirectional
| Cell line | Location | Extract | Total | Ensembl | CAGE | Ens+CAGE | Agreement | |||
|---|---|---|---|---|---|---|---|---|---|---|
| Bi | Uni | Bi | Uni | Bi | Uni | (%) | ||||
| GM12878 | Cytosol | PolyA- | 3,531 | 723 | 2,808 | 414 | 3,117 | 318 | 2,712 | 85.8 |
| Nucleolus | Total | 5,244 | 1143 | 4,101 | 926 | 4,318 | 641 | 3,816 | 85.0 | |
| H1hESC | Cell | PolyA- | 6,041 | 1236 | 4,805 | 889 | 5,152 | 728 | 4,644 | 88.9 |
| HepG2 | Cytosol | PolyA- | 4,315 | 899 | 3,416 | 435 | 3,880 | 378 | 3,359 | 86.6 |
| Nucleolus | Total | 5,169 | 1102 | 4,067 | 798 | 4,371 | 561 | 3,830 | 84.9 | |
| HUVEC | Cytosol | PolyA- | 5,072 | 1107 | 3,965 | 674 | 4,398 | 603 | 3,894 | 88.7 |
| K562 | Cytosol | PolyA- | 4,500 | 893 | 3,607 | 423 | 4,077 | 363 | 3,547 | 86.9 |
| Nucleolus | Total | 2,839 | 678 | 2,161 | 411 | 2,428 | 335 | 2,085 | 85.2 | |
| NHEK | Cytosol | PolyA- | 3,521 | 722 | 2,799 | 352 | 3,169 | 292 | 2,739 | 86.1 |
The number of active protein-coding genes for each cell line and RNA isolation condition (subcellular location and RNA extract). These genes were annotated as bi- or unidirectional using CAGE, Ensembl, or both methods. The agreement between the CAGE and Ensembl annotations is provided for each dataset.