Table 5 Top 10 most downregulated genes in IMF versus SC that are probably not attributable to LD contamination (IMF expression lower than LD). All values are log2 normalised mean expression. P values are reported for both DE and PIF (based on the SC versus IMF comparison)
Gene | Probe | LD | IMF | SC | Inter | Kid | Omen | P value (DE / PIF) |
|---|---|---|---|---|---|---|---|---|
ANGPTL4 | A_73_101924 | 14.49 | 14.41 | 15.03 | 14.77 | 14.67 | 14.89 | 0.0168 / 0.00321 |
IGFBP5 | A_73_110179 | 14.65 | 14.62 | 15.20 | 14.79 | 14.44 | 14.71 | 0.0223 / 0.00595 |
HOXA10 | A_73_104882 | 6.99 | 6.93 | 8.03 | 6.28 | 7.34 | 5.61 | 0.000265 / 0.0133 |
KLK9 | A_73_117770 | 8.93 | 8.44 | 9.33 | 8.39 | 8.15 | 8.18 | 0.00197 / 0.0154 |
BRE | A_73_P052356 | 15.27 | 15.07 | 15.56 | 14.92 | 15.00 | 15.02 | 0.0456 / 0.0216 |
PRSS23 | A_73_111432 | 14.05 | 14.03 | 14.53 | 14.17 | 13.75 | 14.18 | 0.0403 / 0.0166 |
C2CD4B | A_73_P047791 | 11.58 | 11.41 | 12.00 | 11.43 | 11.40 | 12.65 | 0.0223 / 0.0278 |
GPX4 | A_73_106948 | 14.42 | 14.29 | 14.76 | 14.52 | 14.62 | 14.49 | 0.0485 / 0.0291 |
ZCCHC12 | A_73_112381 | 14.97 | 14.57 | 15.02 | 14.26 | 14.30 | 14.43 | 0.0515 / 0.0294 |
FAM71A | A_73_P048226 | 4.36 | 4.18 | 5.39 | 4.65 | 5.12 | 5.99 | 0.0000769 / 0.0515 |