Table 3.
The gene expression changes of DNA damage repair factors in response to intracellular organelle stress.
| Endoplasmic reticulum stress | Endoplasmic reticulum stress | Golgi stress | Lysosome stress | Lysosome stress | Endosome stress | Mitochondrial stress | Mitochondrial stress | Autophagy | Autophagy | |
|---|---|---|---|---|---|---|---|---|---|---|
| GEO ID | GSE49598 | GSE11322 | GSE75150 | GSE39621 | GSE56102 | GSE67227 | GSE40207 | GSE60413 | GSE67676 | GSE13512 |
| Tissue | Mouse embryonic fibroblast | Mouse telencephalon | Mouse embryonic fibroblast | Mouse brain | Human embryonal carcinoma NTERA2 D/1 cells | Mouse liver | Mouse testis | Mouse cerebellum | Mouse liver | Mouse paneth cells |
| Comparison | Perk-/- vs. wild-type mice | Xbp1-/- vs. wild-type mice | Atf4-/- vs. wild-type mice | Npc1-/- vs. Npc1+/- mice | VAMP7 knockdown siRNA vs. control | Rab5-/- vs. wild-type mice | ClpP-/- vs. wild-type mice | Pink1-/- vs. wild-type mice | Atg7 conditional knock out vs. wild-type mice | Atg1611 mutant vs. wild-type mice |
| MGMT | ||||||||||
| ALKBH2 | ||||||||||
| ALKBH3 | ||||||||||
| OGG1 | 3.53 | |||||||||
| NEIL1 | ||||||||||
| MUTYH | ||||||||||
| UNG | 2.18 | |||||||||
| SMUG1 | ||||||||||
| MPG | ||||||||||
| APEX1 | ||||||||||
| APEX2 | ||||||||||
| POLB | ||||||||||
| PNKP | ||||||||||
| XPC | 2.00 | 2.21 | 2.54 | |||||||
| RAD23B | 0.43] | 0.33 | ||||||||
| XPA | ||||||||||
| ERCC2 | ||||||||||
| ERCC3 | ||||||||||
| ERCC1 | ||||||||||
| ERCC5 | ||||||||||
| ERCC4 | 0.25 | 0.38 | ||||||||
| LIG1 | 0.50 | 2.36 | 2.23 | 3.79 | ||||||
| ERCC8 | 0.43 | |||||||||
| ERCC6 | ||||||||||
| XRCC2 | 0.42 | 2.87 | ||||||||
| XRCC3 | ||||||||||
| BRCA2 | 2.17 | |||||||||
| RAD52 | ||||||||||
| RAD51 | 3.75 | 2.83 | 2.05 | |||||||
| LIG4 | ||||||||||
| NHEJ1 | ||||||||||
| XRCC4 | ||||||||||
| XRCC1 | ||||||||||
| LIG3 | 0.41 | 0.21 | ||||||||
| MLH1 | ||||||||||
| MLH3 | 3.18 | |||||||||
| MSH2 | 2.18 | 3.09 | ||||||||
| MSH3 | 2.01 | 0.38 | ||||||||
| MSH6 | ||||||||||
| PMS1 | ||||||||||
| PMS2 | 2.95 | |||||||||
| HMGB1 | 3.19 | |||||||||
| Up | 4/42 | 0 | 2/42 | 0 | 0 | 2/42 | 7/42 | 0 | 2/42 | 2/42 |
| Down | 2/42 | 0 | 1/42 | 1/42 | 0 | 0 | 4/42 | 2/42 | 0 | 0 |
-Genes with significant expression changes (P < 0.05) are shown here. Red text stands for upregulation (FC ≥2), green text stands for downregulation (FC ≤ 0.5).
Perk, protein kinase RNA-like endoplasmic reticulum (ER) kinase; Xbp1, X box-binding protein 1; Atf4, activating transcription factor 4; Npc1, Niemann Pick type C 1; Rab5, Ras-related protein Rab-5A; ClpP, ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit; Pink1, PTEN induced putative kinase 1; Atg7, Autophagy related 7; Atg16l1, Autophagy related 16-like 1; VAMP7, vesicle-associated membrane protein 7.