Table 1.
Individual HERV loci modulated in the presence of HIV infection.
| ID 1 | Group | TPM HIV- | TPM HIV+ | FC | Coordinates (hg38) | St. | Colocalized Genes 2 |
TPM HIV- |
TPM HIV+ |
FC |
|---|---|---|---|---|---|---|---|---|---|---|
| HERV loci upregulated in HIV+ cells | ||||||||||
| 4594 | HERVH | 0.12 | 1.45 | 11.9 | 19:5548576-5553212 | + | ||||
| 3166 | HERVH | 0.12 | 1.07 | 8.9 | 9:131547214-131551936 | + | PRRT1B (+) | 0.04 | 0.21 | 4.9 |
| 2307 | HERV30 | 0.35 | 1.90 | 5.4 | 6:118617102-118626802 | + | CEP85L (-) | 0.34 | 0.49 | 1.4 |
| 2082 | HERV9 | 0.25 | 1.38 | 5.4 | 6:16455730-16464625 | + | ATXN1 (-) | 0.04 | 0.03 | 1.2 |
| 4457 | HML6 | 0.31 | 1.56 | 4.9 | 17:43872528-43874324 | + | ||||
| 1744 | HERVH | 2.91 | 10.11 | 3.5 | 5:702471-708501 | + | ||||
| 3112 | PABL | 0.45 | 1.32 | 3.0 | 9:94265146-94270221 | - | ZNF169 (+) | 0.01 | 0.01 | - |
| HERV loci downregulated in HIV+ cells | ||||||||||
| 691 | HML6 | 1.97 | 0.10 | 19.2 | 2:136071818-136077261 | - | ||||
| 5407 | HML6 | 2.29 | 0.17 | 13.1 | X:57102981-57109396 | + | ||||
| 2658 | HERVH | 2.52 | 0.21 | 12.1 | 7:143105117-143110504 | + | ||||
| 4741 | HERVH | 22.77 | 2.16 | 10.5 | 19:46102204-46109974 | - | ||||
| 2476 | HML3 | 3.21 | 0.32 | 10.1 | 7:43859699-43864985 | - | ||||
| 3788 | HERVH | 3.39 | 0.39 | 8.8 | 12:48111344-48115676 | - | PFKM (+) | 8.66 | 4.88 | 1.8 |
| 6q27b | HERVW | 4.33 | 0.55 | 7.9 | 6:166891083-166898253 | + | AL159163.1 (-) | 0.00 | 0.00 | - |
| 4511 | MER57 | 1.07 | 0.15 | 7.1 | 18:13700682-13708050 | + | FAM210A (-) | 0.11 | 0.07 | 1.5 |
| 5387 | HML6 | 41.38 | 6.53 | 6.3 | X:53159114-53163826 | - | ||||
| 3637 | HUERSP2 | 2.23 | 0.35 | 6.3 | 11:108198480-108204806 | + | ||||
| 933 | HERVH | 3.55 | 0.58 | 6.1 | 3:44344658-44350393 | - | TCAIM (+) | 0.28 | 0.17 | 1.6 |
| 957 | HERV9 | 1.78 | 0.29 | 6.1 | 3:51742261-51747980 | + | ||||
| 5815 | HERVFB | 39.41 | 6.51 | 6.1 | 1:8921052-8927320 | + | ||||
| 4329 | HERVH | 1.56 | 0.29 | 5.4 | 15:101072487-101078293 | + | LRRK1 (+) | 0.18 | 0.17 | 1.08 |
| 3436 | HUERSP3 | 5.73 | 1.16 | 5.0 | 11:34897477-34907140 | + | APIP (-) | 0.68 | 0.52 | 1.3 |
| 1113 | HERVH | 3.24 | 0.70 | 4.6 | 3:128959818-128965400 | + | KIAA1257 (-) | 1.83 | 1.46 | 1.3 |
| 4374 | HERVT | 13.98 | 3.07 | 4.5 | 16:35267618-35277076 | - | ||||
| 1407 | HERVH | 8.37 | 1.84 | 4.5 | 4:54020079-54025546 | + | CHIC2 (-) | 0.05 | 0.00 | - |
| 5356 | HML8 | 2.70 | 0.59 | 4.5 | X:46486517-46490287 | - | KRBOX4 (+) | 0.07 | 0.06 | 1.2 |
| 2334 | HERVH | 18.93 | 4.45 | 4.3 | 6:130192311-130198222 | + | SAMD3 (-) | 0.23 | 0.16 | 1.4 |
| 3887 | HML5 | 1.85 | 0.46 | 4.0 | 12:100159365-100165461 | - | GOLGA2P5 (-) | 0.78 | 0.23 | 3.5 |
| 18p11.21 | HERVW | 1.95 | 0.48 | 4.0 | 18:4681680-4692409 | + | ||||
| Xp11.21 | HERVW | 2.47 | 0.63 | 3.9 | X:7699169-7704068 | - | ||||
| 2219 | HML1 | 5.49 | 1.45 | 3.8 | 6:78854118-78858747 | + | ||||
| 1549 | HML5 | 1.75 | 0.46 | 3.8 | 4:106109837-106114668 | + | TBCK (-) | 2.58 | 1.56 | 1.7 |
| 4475 | HERVH | 1.16 | 0.32 | 3.6 | 17:55467773-55476512 | + | SMIM36 (-) | 0.00 | 0.00 | - |
| 3370 | HERVH | 4.52 | 1.29 | 3.5 | 10:120844932-120850561 | + | WDR11-AS1 (-) | 0.29 | 0.14 | 2.1 |
| 1975 | HERVH | 14.08 | 4.34 | 3.2 | 5:124966686-124972226 | - | LINC02240 (+) | 0.01 | 0.01 | - |
| 3701 | HERVH | 8.68 | 2.68 | 3.2 | 12:9962437-9968690 | - | CLEC12A (+) | 0.20 | 0.13 | 1.6 |
| 5705 | HERVH | 7.88 | 2.53 | 3.1 | X:131712025-131717764 | + | FIRRE (-) | 0.00 | 0.00 | - |
| 3544 | HERVE | 2.09 | 0.69 | 3.0 | 11:71886034-71890084 | + | AP002495.1 (-) | 0.04 | 0.00 | - |
| 4610 | HERVH | 1.96 | 0.64 | 3.0 | 19:9635997-9642066 | - | ZNF561-AS1 (+) | 0.21 | 0.54 | 2.6 |
1 ID referred to Vargiu et al. 2016, except for HERV-W locus names that come from Grandi et al. 2016. 2 Based on Genecode annotations (version 32). FC = Fold Change, St. = Strand. TPM values are represented with a color gradient from red (highest) to green (lowest).