Table 2.
Genomic and transcriptomic features of the 6 probesets of interest.
| HERV Probesetsa | ||||||
|---|---|---|---|---|---|---|
| Transcriptomic & genomic features | 1556107_at | 230354_at | 1553043_a_at | 1560527_at | 1559777_at | 236982_at |
| Patients vs. HVs | UP | UP | UP (for Burn & SS2) | UP (for SS1 & SS2) | UP | UP |
| log2FCb in | ||||||
| Burn | 1.13 | 1.73 | 1.48 | −0.55 | 1.05 | 0.77 |
| Trauma | 1.31 | 1.47 | −0.33 | 1.50 | 0.79 | 1.57 |
| SS1 | 0.57 | 2.03 | 0.26 | 0.72 | 1.07 | 0.90 |
| SS2 | 1.45 | 2.97 | 1.08 | 2.00 | 1.26 | 1.12 |
| Confirmedc | Yes* | Yes* | Yes* | Yes* | No | No |
| HERV family | MLT1H | LTR33 | MLT1D | LTR101_Mam | LTR16B2 | ERV24B_Prim-int |
| HERV coordinatesd | chr1 207372720-207272854 | chr2 40545338-40545778 | chr17 74694268-74694744 | chr7 102988743-102988923 | chr4 184844993-184845324 | chr21 44875454-44876122 |
| Closest gene | CD55 | SLC8A1 | CD300LF | NFE4 | MIR3945HG | PTTG1IP |
| Localizatione | 3′ UTR | intron 1 | 3′UTR | 3′end | 3′ UTR | promoter region |
a
HGU133plus2 Affymetrix probesets mapping on a HERV locus.
b
A positive log2 FC means that the probeset is more expressed in patients than in HV.
c
Confirmed by RT-qPCR.
*
Expression confirmed. Modulation between patients and HV not always statistically confirmed, mainly due to high inter-individual variability.
d
Grch38 genomic coordinates of HERV locus.
e
Localization of HERV element according to the nearby gene.