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. 2012 Jun 28;7(6):e40194. doi: 10.1371/journal.pone.0040194

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
a

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.

b

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.

c

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.

d

Subsets of complete or partial proviruses.

e

One element can be composed of several probesets.