Table 2.
Microarray-based differential expression of the most significant HERV probesetsa
| Probesetsb | Familyb | Copy positionc | Global analysisd |
Pairwise comparaisone |
|||
|---|---|---|---|---|---|---|---|
| raw p-value | q-value | expression levels | fold change | ||||
| Placenta | Others | Placenta | |||||
| HW28073.L5.U5_at | HERV-W | (−) chr7: 91935211–91945442 | 0.00E+00 | 0.00E+00 | 38.4 | 393.9 | 10.25 |
| envw_at | HERV-W | (–) chr7: 91935211–91945442 | 0.00E+00 | 0.00E+00 | 25 | 273.8 | 10.95 |
| sp.ervwe1_at | HERV-W | (–) chr7: 91935211–91945442 | 0.00E+00 | 0.00E+00 | 33.2 | 1014.8 | 30.57 |
| envfrd_at | HERV–FRD | (–) chr6: 11210982–11215545 | 1.16E–06 | 7.43E–06 | 10.7 | 95.4 | 8.92 |
| envR_at | ERV3/HERV–R | (–) chr7: 64088729–64097156 | 6.77E–05 | 4.14E–05 | 56.9 | 127.8 | 2.25 |
| Tumoral colon | Colon N | Colon T | |||||
| HH34532.L5.U5_at | HERV–H | (+) chr1: 68624274–68630265 | 9.70E–07 | 7.39E–06 | 9.9 | 14.1 | 1.42 |
| envH3_at | HERV–H | (+) chr2: 155436773–155438869 | 6.01E–06 | 1.54E–05 | 32.7 | 181.2 | 5.54 |
| Tumoral testis | Testis N | Testis T | |||||
| HW28073.L5.U5_at | HERV–W | (–) chr7: 91935211–91945442 | 0.00E+00 | 0.00E+00 | 29.9 | 202.6 | 6.78 |
| envw_at | HERV–W | (–) chr7: 91935211–91945442 | 0.00E+00 | 0.00E+00 | 12.1 | 154.9 | 12.80 |
| sp.ervwe1_at | HERV–W | (–) chr7: 91935211–91945442 | 0.00E+00 | 0.00E+00 | 21.1 | 268.6 | 12.73 |
| HW08822.L5.U5_at | HERV-W | (–) chr4: 41982210–41989670 | 0.00E+00 | 0.00E+00 | 76.9 | 984 | 12.80 |
| HW13386.L5.U5_at | HERV–W | (+) chr13: 68693758–68697469 | 3.88E–07 | 3.67E–06 | 54.9 | 428.4 | 7.80 |
| HW38223.L5.U5_at | HERV–W | (+) chr2: 17383688–17391462 | 3.88E–07 | 3.67E–06 | 18.3 | 211.4 | 11.55 |
| HW33438.L5.U5_at | HERV–W | (+) chr21: 27148626–27156169 | 3.88E–07 | 3.67E–06 | 27.1 | 203.9 | 7.52 |
| HW22795.LS.U5_at | HERV–W | (+) chrX: 113026617–113027400 | 2.91E–06 | 1.33E–05 | 49.5 | 292.2 | 5.90 |
| envk5_at | HML-2 | (–) chr5: 156018263–156019973 | 3.10E–06 | 1.33E–05 | 14.6 | 105.3 | 7.21 |
| envk6_at | HML-2 | (–) chr8: 7343775–7351309 | 3.10E−06 | 1.33E−05 | 47.3 | 411.7 | 8.70 |
| H2035746.GAG_at | HML-2 | (–) chr12: 57008477–57015997 | 3.88E−07 | 3.67E−06 | 18.4 | 164.6 | 8.95 |
| Tumoral prostate | Prostate N | Prostate T | |||||
| envR_at | ERV3/HERV-R | (–) chr7: 64088729–64097156 | 6.77E–05 | 4.14E–05 | 41 | 99 | 2.41 |
aOnly the most significant probesets identified by global SAM analysis are presented. Probesets are classified according to the site in which the overexpression is observed.
bThe names of the probeset and HERV family are indicated.
cThe orientation of the copy onto the DNA strand, the chromosome number, and the positions of the first and terminal bases of the copy on the chromosome are indicated (UCSC genome March 2006 version 36.1).
dRaw p– and q–value summarized the results of the global analysis among all the samples. The raw p–value was obtained by SAM multiclass test and q–value was the lowest False Discovery Rate at which the probeset was considered significant.
eFor pairwise comparison, the reference conditions are defined by either the corresponding normal tissue for tumoral site of overexpression, or by all non–placenta normal tissues for placenta. The expression levels are summarized by the median values. The degree of differential expression between reference and overexpressed sites is expressed as fold change.