TABLE 1.
Results for the 31 key deHERV loci that showed significant modulation in all analysesa
| 31 Common deHERVs |
Results from RTP vs C |
Results from C vs HC |
Results from RTP vs HC |
Colocalized de-genes (results from global comparison) |
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID | Group | Log2 FC | P-adj | del2 | Log2 FC | P-adj | del2 | Log2 FC | P-adj | del2 | Gene name | Prot. coding | del2 | Log2 FC | P-adj |
| 2776 | HERVE | –2.5 | 1.15E-22 | DEL − | 3.5 | 1.31E-43 | DEL + | 1 | 1.83E-05 | DEL + | |||||
| 2135 | HML3 | –4.6 | 9.08E-20 | DEL − | 6.9 | 2.01E-31 | DEL + | 2.3 | 0.0001827 | DEL + | |||||
| 2q11.2 | HERVW | −3 | 2.84E-15 | DEL − | 1.1 | 0.0036475 | DEL + | −1.9 | 4.63E-08 | DEL − | |||||
| 5860 | HERVFB | −3.3 | 4.18E-15 | DEL − | 1.4 | 2.40E-05 | DEL + | −1.9 | 1.38E-05 | DEL − | AL591845.1 | no | DEL − | −1.21 | 0.009788 |
| 4613 | HERVH | 1.9 | 9.15E-10 | DEL + | −3.1 | 3.99E-25 | DEL − | −1.2 | 9.67E-09 | DEL − | |||||
| 15q15.1 | HML8 | 1.6 | 3.51E-09 | DEL + | –2.7 | 1.46E-26 | DEL − | –1.1 | 4.54E-07 | DEL − | RAD51-AS1 | no | DEL − | −1.13 | 1.42E-07 |
| 2574 | HERVE | 1.9 | 1.16E-08 | DEL + | –3.5 | 1.02E-28 | DEL − | −1.6 | 2.46E-11 | DEL − | AC079781.5 | no | DEL − | −1.21 | 1.92E-06 |
| 3052 | HERVH | –1.7 | 3.31E-07 | DEL − | −1.3 | 3.64E-06 | DEL − | –2.9 | 2.96E-28 | DEL − | AL355377.4 | no | DEL − | −2.79 | 2.46E-11 |
| 6228 | HERVIP | 2.9 | 1.98E-06 | DEL + | –5.4 | 2.74E-21 | DEL − | −2.5 | 1.22E-08 | DEL − | |||||
| 3107 | HERVH | –1.2 | 4.54E-06 | DEL − | −1.3 | 1.94E-07 | DEL − | −2.5 | 2.15E-31 | DEL − | |||||
| 6171 | HML2 | 1.5 | 2.83E-05 | DEL + | −2.7 | 5.19E-16 | DEL − | −1.2 | 7.31E-05 | DEL − | |||||
| 6116 | LTR39 | −2.2 | 3.03E-05 | DEL − | 5.3 | 2.22E-11 | DEL + | 3.2 | 0.0001674 | DEL + | |||||
| 3192 | HML2 | 4.6 | 4.92E-05 | DEL + | −6.3 | 1.80E-09 | DEL − | −1.8 | 0.0015817 | DEL − | |||||
| 6q27b | HERVW | 1.7 | 0.000101 | DEL + | −2.8 | 6.48E-12 | DEL − | −1.1 | 0.0010291 | DEL − | |||||
| 5361 | HERVE | 1.5 | 0.000108 | DEL + | −2.7 | 2.16E-14 | DEL − | −1.2 | 2.19E-06 | DEL − | |||||
| 3387 | HERVIP | 2.5 | 0.000139 | DEL + | –4.6 | 6.85E-15 | DEL − | −2.2 | 2.84E-06 | DEL − | |||||
| 1091 | MER41 | –2.4 | 0.00015 | DEL − | 5.2 | 9.49E-10 | DEL + | 2.8 | 0.0027002 | DEL + | |||||
| 19p13.2b | HML6 | 2 | 0.000165 | DEL + | −3.8 | 1.87E-15 | DEL − | −1.8 | 2.61E-07 | DEL − | |||||
| 3165 | HERVFA | –1.9 | 0.000226 | DEL − | 6.2 | 1.64E-14 | DEL + | 4.3 | 1.90E-07 | DEL + | |||||
| 4491 | MER41 | –2.7 | 0.000548 | DEL − | 5.5 | 1.87E-09 | DEL + | 2.8 | 0.0059368 | DEL + | COLEC12 | Yes | DEL + | 1.99 | 0.006223 |
| 3949 | HERVE | 1 | 0.000575 | DEL + | –2.8 | 2.70E-26 | DEL − | –1.8 | 2.95E-16 | DEL − | AL590064.1 | No | DEL − | −1.31 | 3.24E-08 |
| FLVCR2 | Yes | DEL + | 2.37 | 2.39E-08 | |||||||||||
| 2153 | HML2 | −2.5 | 0.000627 | DEL − | 6.2 | 8.28E-12 | DEL + | 3.7 | 7.13E-05 | DEL + | TNFRSF21 | Yes | DEL + | 2.08 | 6.27E-06 |
| 4332 | HML3 | 1.1 | 0.000803 | DEL + | −2.6 | 1.04E-18 | DEL − | −1.5 | 4.31E-09 | DEL − | AC108134.3 | No | DEL − | −1.28 | 7.85E-07 |
| 2319 | Unclassifiable | −2.3 | 0.001278 | DEL − | 5.4 | 5.66E-10 | DEL + | 3.1 | 0.0008136 | DEL + | |||||
| 4745 | HERVH | −1.4 | 0.001808 | DEL − | −1 | 0.0088384 | DEL − | −2.4 | 3.23E-12 | DEL − | |||||
| 3q25.1a | HERVW | 3.5 | 0.002572 | DEL + | –5.4 | 5.59E-07 | DEL − | −1.8 | 0.0026058 | DEL − | |||||
| 3366 | HERVH | –1.9 | 0.002919 | DEL − | 6 | 2.58E-12 | DEL + | 4.1 | 3.11E-06 | DEL + | |||||
| 3757 | HERVI | −2 | 0.00398 | DEL − | 5.4 | 9.41E-10 | DEL + | 3.4 | 0.0002105 | DEL + | |||||
| 5410 | HERVH48 | 2.5 | 0.006516 | DEL + | −6.1 | 1.85E-14 | DEL − | −3.6 | 6.91E-33 | DEL − | Z83745.1 | No | DEL − | −3.64 | 8.28E-25 |
| 933 | HERVH | 1.5 | 0.006929 | DEL + | –3.7 | 3.60E-14 | DEL − | −2.2 | 1.60E-07 | DEL − | |||||
| 14q32.11 | HERVW | 1.9 | 0.007315 | DEL + | –3.3 | 2.36E-07 | DEL − | −1.4 | 0.0039035 | DEL − | |||||
a
The table shows the results of differential expression analysis as performed in pairwise comparisons of the expression between RTP and C SARS-CoV-2-exposed individuals, C and HC, and RTP and HC. The results for the eventual colocalized genes, when significantly modulated, are also reported and refer to the overall comparison (C and RTP individuals versus HC). FC, fold change; del2, the observed modulation: DEL+ indicates upregulation while DEL− indicates downregulation; prot., protein.