Table 1.
Data used in evaluating the SCOREM algorithm
| Experiment | Tissue type | Conditions | Platform | Source (Rawa) | No. of samples |
|---|---|---|---|---|---|
| GSE3678b | Thyroid | Tumor versus normal | Human Genome U133 Plus 2.0 (GPL570) | GEO (yes) | 14 |
| GSE4051 (11) | Retina | Nrl-knockout versus wild-type at 5 time points in development | Mouse Genome 430 2.0 (GPL1261) | GEO (yes) | 39 |
| GSE4799 (12) | Spermatogonial stem cells | Growth factor restoration (3 time points) versus withdrawal and baseline | Mouse Genome 430 2.0 (GPL1261) | GEO (no) | 15 |
| GSE9371 (13) | Aorta | Estrogen versus placebo in wild type, ERα- and ERβ- knockouts | Mouse Genome 430 2.0 (GPL1261) | GEO (yes) | 22 |
| BrCac (14–16) | Breast cancer (MCF7 cell line) | Estrogen versus placebo at 2 time points | Human Genome U133A (GPL96) | GEO (no) | 26 |
| VSMC (17) | Aorta | Estrogen versus placebo at 3 time points | Mouse Genome 430A 2.0 (GPL339) | Authors (yes) | 18 |
| GonFat (18) | Gonadal fat | Female versus male and female versus ovarioectomized female | Mouse Genome 430 2.0 (GPL1261) | Authors (yes) | 21 |
| IngFat (18) | Inguinal fat | Female versus male and female versus ovarioectomized female | Mouse Genome 430 2.0 (GPL1261) | Authors (yes) | 21 |
aWhether or not raw data (.CEL files) were available or only preprocessed data.
bReyes et al. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3678.