Table 1.
GEO identifiers and data sets used for pathway activation method comparison
| GEO ID | Subgroup 1 (Baseline) | Subgroup 2 |
| GDS1062 | Metastasis-negative squamous cell carcinoma (8) | Metastasis-positive squamous cell carcinoma (14) |
| GDS1067 | Monoclonal gammopathy (7) | Multiple myeloma (39) |
| GDS1210 | Normal gastric tissue (8) | Gastric carcinoma (14) |
| GDS1220 | Normal pleural tissue (8) | Malignant mesothelioma (40) |
| GDS1221 | Peripheral blood, CML responsive Gleevec (9) | Peripheral blood, CML not responsive Gleevec (7) |
| GDS1231 | Enriched for hematopoietic stem cells (9) | Enriched for committed hematopoietic cells (9) |
| GDS1329 | 'Basal' breast tumors (16) | 'Luminal' breast tumors (27) |
| GDS1329 | 'Basal' breast tumors (16) | 'Apocrine' breast tumors (6) |
| GDS1332 | Whole blood normal controls (14) | Whole blood symptomatic Huntington disease (12) |
The numbers in parentheses are the number of samples in each subgroup. CML, chronic myelogenous leukemia. References are provided in the main text.