TABLE 1.
GEO dataset study population characteristics. The GEO microarray datasets included in this study are indicated. Of those which met the quality criteria, four datasets were available for HNSCC, four for PDAC, and five for gastric cancer (referred to as STAD in the manuscript). Samples comprised tumor and adjacent tissue or healthy biopsy. For the analysis of the dataset GSE138206, control samples consisted of contralateral normal samples; in this study the tissue adjacent to cancer was excluded. Abbreviations: GEO, Gene Expression Omnibus database; HNSCC, head and neck squamous cell carcinoma; PDAC, pancreatic ductal adenocarcinoma; STAD, stomach adenocarcinoma; GC, gastric cancer; OSCC, oral squamous cell carcinoma.
| Cancer type | Dataset | Tumor/normal | Tumor/normal type | Platform (# probes) | Author, year |
|---|---|---|---|---|---|
| Head and neck squamous cell carcinoma cancer tumor: 114/control: 106 | GSE138206 | 6/6 | OSCC tumor/contralateral normal | GPL570 (54,675) | Pan H. et al., 2019 |
| GSE23036 | 63/5 | Pre-treatment HNSCC biopsy/healthy tissue | GPL571 (22,277) | Pavon et al. (2012) | |
| GSE31056 | 23/73 | OSCC tumor/adjacent tissue | GPL10526 (17,788) | Reis et al. (2011) | |
| GSE6631 | 22/22 | HNSCC tumor/adjacent tissue or contralateral normal | GPL8300 (12,625) | Kuriakose et al. (2004) | |
| Pancreatic ductal adenocarcinoma tumor: 189/control: 161 | GSE15471 | 39/39 | PDAC tumor/adjacent tissue | GPL570 (54,675) | Badea et al. (2008) |
| GSE16515 | 36/16 | Pancreatic tumor/adjacent tissue | GPL570 (54,675) | Pei et al. (2009) | |
| GSE28735 | 45/45 | PDAC tumor/adjacent tissue | GPL6244 (33,297) | Zhang et al. (2012) | |
| GSE62452 | 69/61 | PDAC tumor/adjacent tissue | GPL6244 (33,297) | Yang et al. (2016) | |
| Gastric cancer tumor: 203/control: 84 | GSE103236 | 10/9 | GC tumor/adjacent tissue | GPL4133 (45,220) | Economescu et al. (2010) |
| GSE33651 | 40/12 | GC tumor/healthy biopsy | GPL2895 (56,448) | Park et al. (2011) | |
| GSE54129 | 111/21 | GC tumor/healthy biopsy | GPL570 (54,675) | Lui B. et al., 2014 | |
| GSE65801 | 32/32 | GC tumor/adjacent tissue | GPL14550 (42,545) | Li et al. (2015) | |
| GSE79973 | 10/10 | GC tumor/adjacent tissue | GPL570 (54,675) | He et al. (2016) |