Table 1. Detection of the HERV transcriptome.
Repertoire | Elementse | HERV-W | HERV-H | HERV-E 4.1 | HERV-FRD | HERV-KHML-2 | HERV-K HML-5 | Total |
Genome a | solo LTRs | 464 | 1079 | 158 | 1259 | 1000 | 87 | 4047 |
complete or partial proviruses | 823 | 1492 | 455 | 349 | 2685 | 184 | 5988 | |
5′ LTRsd | 128 | 1036 | 41 | 36 | 52 | 22 | 1315 | |
3′ LTRsd | 219 | 1062 | 39 | 45 | 2482 | 22 | 3869 | |
gagd | 199 | 1093 | 246 | 88 | 117 | 126 | 1869 | |
ppold | 234 | 0 | 0 | 96 | 0 | 0 | 330 | |
pold | 0 | 1315 | 330 | 75 | 155 | 147 | 2022 | |
envd | 240 | 1173 | 67 | 154 | 2548 | 97 | 4279 | |
Chip b | solo LTRs | 432 | 553 | 120 | 1189 | 512 | 77 | 2883 |
complete or partial proviruses | 304 | 1354 | 427 | 218 | 215 | 172 | 2690 | |
5′ LTRsd | 120 | 444 | 29 | 33 | 29 | 18 | 673 | |
3′ LTRsd | 171 | 485 | 29 | 43 | 85 | 19 | 832 | |
gagd | 162 | 787 | 228 | 80 | 85 | 125 | 1467 | |
ppold | 222 | 0 | 0 | 0 | 0 | 0 | 222 | |
pold | 0 | 1154 | 307 | 35 | 93 | 135 | 1724 | |
envd | 205 | 513 | 63 | 127 | 66 | 97 | 1071 | |
Transcriptome c | solo LTRs | 100 | 209 | 30 | 251 | 199 | 19 | 808 |
complete or partial proviruses | 101 | 587 | 91 | 39 | 75 | 17 | 910 | |
5′ LTRsd | 26 | 154 | 10 | 8 | 10 | 4 | 212 | |
3′ LTRsd | 43 | 182 | 10 | 11 | 35 | 7 | 288 | |
gagd | 12 | 202 | 51 | 4 | 15 | 4 | 288 | |
ppold | 8 | 0 | 0 | 0 | 0 | 0 | 8 | |
pold | 0 | 170 | 28 | 1 | 9 | 2 | 210 | |
envd | 49 | 71 | 5 | 16 | 12 | 2 | 155 |
Number of distinct genomic HERV loci included in HERV database HERV-gDB3. The database contains 6 HERV families with unequal input. The search for distinct elements belonging to each family is performed by systematic BLAST genome coverage, allowing a maximum 20% divergence with prototype elements.
Number of distinct genomic HERV loci present in the chip. Each element of the database is processed through home-made EDA+ algorithm to find probes that match optimal hybridization criteria. The candidate probes are then checked against the entire human genome (NCBI 36/hg18) using the KASH algorithm to control their cross-hybridizing ability and non-specific sequences are removed. Probes are ultimately assembled into probesets to discriminate individual genomic HERV sequences. Differences between database and chip mark the success in designing HERV-specific probes and probesets. For clarity, the probeset content is not detailed.
HERV transcriptome results: number of active elements in all tissues tested. After the experiments were normalized using the COMBAT method and an arbitrary positive threshold was applied (value = 100), elements that are active in at least one tissue are enumerated.
Subsets of complete or partial proviruses.
One element can be composed of several probesets.