Table 1.
Number of elements and functional sub-regions contained in HERVgDB4 (left) and designed on HERV-V3 (right) where one probeset is defined by sub-region
| Repertoire | HERVgDB4 (database) | HERV-V3 (array) | |||
|---|---|---|---|---|---|
| Number of elements | Number of sub-regions | Number of elements | Number of probesets | Number of elements | |
| HERV prototypes | 29,859 | 90,106 | 29,807 | 45,374 | 29,859 |
| HERV centromeric | 192 | 589 | 24 | 29 | 192 |
| HERV Dfam | 169,821 | 342,482 | 154,535 | 283,641 | 169,821 |
| MaLR Dfam | 228,429 | 45,543 | 179,323 | 311,286 | 22,8429 |
| LINE1 | 1072 | 4627 | 664 | 1416 | 1072 |
| lncRNA | 3812 | 3819 | 3777 | 3777 | 3812 |
| Viruses | 291 | 386 | 289 | 368 | 2044 |
| gPEHM | 1559 | 1559 | 1559 | 1559 | 8743 |
| gU133 | 1559 | NA | 1559 | 3884 | 42,964 |
| gHTA | 1559 | NA | 1559 | 35,398 | 344,002 |
| Affymetrix Controls | NA | NA | NA | 177 | 20,895 |
| Total | 435,040 | 898,998 | 372,976 | 686,869 | 2,651,585 |
The discrepancy between the number of elements in the database and on the array is due to cross-hybridizing elements discarded during the design