Table 1 Seven pairs (fourteen in total) of independent microarray datasets used for benchmarking
From: Comparison and evaluation of pathway-level aggregation methods of gene expression data
Phenotype | Dataset name and reference | Class 1 (control group) samples | Class 2 (case group) samples | Data source | Platform |
|---|---|---|---|---|---|
Effect of smoking on bronchial epithelium | Â | Never smokers | Current smokers | Â | Â |
| Â | Beane [18] | 21 | 52 | GSE7895 | U133A |
| Â | Vanni [19] | 22 | 37 | GSE10135 | U133 Plus 2 |
Subtypes of non-small cell lung cancer (NSCLC) | Â | AD (adenocarcinoma) | SCC (squamous cell carcinoma) | Â | Â |
| Â | Bild [20] | 58 | 53 | GSE3141 | U133 Plus 2 |
| Â | Lee [21] | 63 | 75 | GSE8894 | U133 Plus 2 |
Subtypes of primary high grade glioma | Â | AA (anaplastic astrocytoma) | GBM (glioblastoma multiforme) | Â | Â |
| Â | Phillips [22] | 21 | 56 | GSE4271 | U133 Set |
| Â | Sun [23] | 19 | 77 | GSE4290 | U133 Plus 2 |
Estrogen receptor (ER) status in breast cancer | Â | ER-negative | ER-positive | Â | Â |
| Â | Chin [24] | 46 | 84 | E-TABM-158 | U133A |
| Â | Minn [25] | 42 | 57 | GSE2603 | U133A |
Breast cancer grade | Â | Grade 1 | Grade 3 | Â | Â |
| Â | Desmedt [26] | 30 | 83 | GSE7390 | U133A |
| Â | Sotiriou [27] | 28 | 32 | GSE2990 | U133A |
Lung cancer grade | Â | Grade 1 | Grade 3 | Â | Â |
| Â | Dana-Farber [28] | 13 | 37 | Author's website | U133A |
| Â | Michigan [28] | 26 | 66 | Â | Â |
Clear cell renal cell carcinoma (CCRCC) vs Normal kidney | Â | Normal kidney | Tumorous kidney | Â | Â |
| Â | Jones [29] | 23 | 32 | GSE15641 | U133A |
| Â | Kort [30] | 12 | 10 | GSE11024 | U133 Plus 2 |