Table 1.
Gene expression datasets and the main subjects used in this study.
| Data source | Description | Main subjects |
|---|---|---|
| GEO databases | With the confirmed autophagy phenotypes | |
| GSE137359 (N = 8) (12) | Chidamide reverses the B-cell lymphoma chemoresistance by inducing autophagy | Low autophagy: rituximab-resistant/sensitive B cells High autophagy: chidamide-treated cells |
| GSE129203 (N = 8) (13) | GSK343, a potent autophagy inducer, inhibits hepatocellular carcinoma cells | Low: HepG2/PLC5 control cells High: GSK343-induced cells |
| GSE106175 (N = 6) (14) | Suberanilohydroxamic acid (SAHA) with the effects of lysosomal and autophagy activation | Low: control HeLa cells High: SAHA-treated HeLa cells |
| GSE46374 (N = 4) (15) | Atorvastatin inhibits prostate cancer proliferation by inducing autophagy | High: LNCaP/PC3 control cells Low: atorvastatin-treated cells |
| GSE185153 (N = 6) | High: HEK293 control cells Low: autophagy-deficient ATG7−/− HEK293 |
|
| GSE31397 (N = 6) | miR-101-inhibited autophagy can sensitize breast cancer to 4-hydro-xytamoxifen-mediated cell death | High: MCF-7 control cells Low: miR-101 transfection cells |
| TCGA database | Exploring the relationships of autophagy and resistance in various cancer | |
| TCGA Pan-cancer | The standardized Pan-cancer dataset (N = 10,535) from the UCSC database (https://xenabrowser.net/) | Gene correlation analysis, based on the RNA-seq expression data of different genes in various cancer samples’ survival analysis, combined with its prognostic information |
| TCGA-BRCA | Breast cancer (N = 1,034) | |
| TCGA-PRAD | Bladder cancer (N = 396) | |
| TCGA-BLCA | Prostate cancer (N = 491) | |
| TCGA-STAD | Gastric cancer (N = 336) | |
| GEO databases | With the confirmed chemoresistance phenotypes | |
| GSE163361 (N = 84) (16) | Inflammatory breast cancer (SUM149 and FCIBC02 parental, and their paclitaxel-resistant, or doxorubicin-resistant cell lines), in biological triplicates | FCIBC02/SUM149 parental vs. paclitaxel-resistant vs. doxorubicin-resistant cells FCIBC02/SUM149 parental vs. drug-treated (paclitaxel or doxorubicin) FCIBC02/SUM149 chemoresistant cells vs. drug-treated (same concentration) |
| GSE54326 (N = 24) (17) | Breast cancer MDA-MB-231, MCF7, SKBR3, and ZR-75-1 parental and epirubicin-resistant cell lines | Parental vs. epirubicin-resistant, in biological triplicates |
| GSE125187 (N = 9) (18) | Breast cancer MCF-7 and their anthracycline-resistant cells | MCF-7 vs. doxorubicin-resistant vs. epirubicin-resistant cells |
| GSE155478 (N = 6) (19) | MCF-7 vs. doxorubicin-resistant | |
| GSE202536 (N = 15) | Triple-negative breast cancer CAL51 and doxorubicin-resistant | CAL51 vs. doxorubicin-resistant CAL51/CAL51 doxorubicin-resistant cell vs. doxorubicin-treated (same concentration) |