Table 1. Data sets used in the metaanalysis.
| Data set | Platform | Set | Control+treated | Target cells, pretreatment | Inhibitor | |
| 1 | GSE11729 | Affy HG_U133_Plus_2 | 1 | 4+12 | H1299 | gefitinib |
| 2 | 12+12 | H1299, EGF | gefitinib | |||
| 3 | 2+6 | L858R | gefitinib | |||
| 4 | 6+6 | L858R, EGF | gefitinib | |||
| 2 | GSE16179 | Affy HG_U133_Plus_2 | 5 | 3+3 | BT474 | lapatinib |
| 6 | 3+3 | BT474-J4, | lapatinib | |||
| 7 | 3+3 | BT474-J4, forteinib | lapatinib | |||
| 3 | GSE20854 | Affy HG_U133_Plus_2 | 8 | 4+4 | Hec50co | gefiitinib |
| 9 | 4+4 | Ishikawa H | gefiitinib | |||
| 4 | GSE23206 | Affy HG_U133_Plus_2 | 10 | 1+1 | H322c | gefiitinib |
| 5 | GSE30516 | Affy HG_U133_Plus_2 | 11 | 4+9 | BT20 | erlotinib |
| 12 | 3+3 | MD | erlotinib | |||
| 13 | 3+3 | MCF | erlotinib | |||
| 6 | GSE32975 | Affy HG_U133_Plus_2 | 14 | 2+2 | HaCat, EGF | gefiitinib |
| 15 | 2+2 | HaCat, serum | gefiitinib | |||
| 7 | GSE33658 | Affy HG_U133_Plus_2 | 16 | 5+6 | breast cancer biopsies +/− Gefitinib | gefiitinib |
| 8 | GSE6521 | Affy HG_U133_Plus_2 | 17 | 2+7 | MCF7 | AG1478 |
| 18 | 7+7 | MCF7, heregulin | AG1478 | |||
| 9 | GSE8141 | Affy HG_U133_Plus_2 | 19 | 4+4 | MCF7 | gefiitinib |
| 20 | 4+4 | MCF7/HER2-18 | gefiitinib | |||
| 21 | 4+4 | MCF7/HER2-18, Tamoxifen | gefiitinib | |||
| 10 | GSE19500 | Affy HG_U133A | 22 | 4+4 | bronchial epithelial cells | AG1478 |
| 23 | 3+3 | bronchial e.c., high barometric pressure | AG1478 | |||
| 11 | GSE17948 | Affy HGU95v2 | 24 | 3+4 | HMCV-infected monocytes | AG1478 |
| 25 | 3+4 | HMCV-infected monocytes | antiEGFR | |||
| 12 | GSE23428 | Agilent custom array | 26 | 5+5 | triple-negative breast cancer biopsies | cetuximab |
| 13 | GSE32333 | Agilent-027114 | 27 | 3+4 | xenografts of A431 | nimotuzumab |
| 28 | 4+3 | xenografts of A431, Rapamicin | nimotuzumab | |||
| 14 | GSE38302 | Agilent-028004 | 29 | 1+1 | PC-9 | gefiitinib |
| 30 | 3+3 | PC-9GR | gefiitinib | |||
| 15 | GSE38310 | Illumina HumanHT-12 v3.0 | 31 | 3+3 | HCC827 | erlotinib |
| 32 | 3+3 | HCC827-ER3 | erlotinib | |||
| 33 | 3+3 | HCC827-T15-2 | erlotinib | |||
| 16 | GSE38376 | Illumina HumanHT-12 v3.0 | 34 | 3+6 | SKBR3 | lapatinib |
| 35 | 3+6 | SKBR3-R | lapatinib | |||
| 17 | GSE40130 | Illumina HumanHT-12 V4.0 | 36 | 3+3 | FaDu, erlotinib | miR-7 |
| Illumina HumanWG-6 v3.0 | 37 | 2+2 | HN5, erlotinib | miR-7 | ||
| 18 | GSE19043 | Illumina HumanRef-8 v2 | 38 | 3+3 | DiFi | gefitinib |
| 39 | 3+3 | GTL-16 | gefitinib | |||
| 19 | GSE23175 | Illumina HumanRef-8 v2 | 40 | 1+15 | MCF10-A | gefiitinib |
| 41 | 1+15 | MCF10HER | gefiitinib | |||
| 20 | GSE34557 | Illumina HumanWG-6 v3.0 | 42 | 3+3 | human epidermal keratinocytes | AG1478 |
| 43 | 3+3 | human epidermal keratinocytes, BMP2 | AG1478 |
Only samples directly comparing EGFR inhibitor-treated with their control samples were used. The comparisons column designates specific sets of treated and control samples. Note that GSE40130 used two different inhibitors, which were analyzed separately. ‘a’ marks the studies used in the ‘Not-Gefitinib’ set.