Quantile-normalized transcriptomes from control and ligand-treated cell lines (level 3 data)

Ligands / cell lines assayed

In the Connectivity Map data, there are 16 ligands assayed in all 14 cell lines, and 300 ligands assayed in 8 cell lines.

EGF HGF INS IGF2 TGFA IGF1 FGF1 HBEGF IL6 IL4 IFNG BTC GDNF GAS6 TNF IL17A ctrl min.ctrl.ratio
breast_normal_MCF10A 119 62 62 62 62 62 59 61 60 59 60 60 61 60 62 60 196 0.6071429
breast_tumor_BT20 146 74 74 73 74 74 74 74 73 74 73 74 74 69 74 74 273 0.5347985
breast_tumor_HS578T 120 58 59 60 60 60 60 60 60 59 58 57 58 59 55 60 232 0.5172414
breast_tumor_MCF7 153 83 80 80 80 80 80 80 78 78 78 80 79 76 75 75 4389 0.0348599
breast_tumor_MDAMB231 120 58 60 60 60 60 60 60 60 60 59 58 59 59 56 60 251 0.4780876
breast_tumor_SKBR3 123 57 62 62 62 62 62 62 62 62 61 60 58 62 57 62 265 0.4641509
kidney_normal_HA1E 5 10 5 5 5 5 5 5 5 5 5 5 5 5 5 3 1135 0.0088106
large_intestine_tumor_HT29 5 10 5 5 4 4 5 4 5 4 5 4 4 4 5 3 2059 0.0048567
liver_tumor_HEPG2 6 12 6 6 6 6 6 6 6 6 6 6 5 6 6 3 780 0.0153846
lung_normal_HCC515 5 10 5 5 5 5 5 5 5 5 5 5 5 5 5 3 957 0.0104493
lung_tumor_A549 6 12 6 6 6 6 6 5 6 5 6 6 6 6 6 3 2847 0.0042150
prostate_tumor_PC3 5 7 5 5 4 4 5 5 4 5 5 5 3 4 5 5 4060 0.0017241
prostate_tumor_VCAP 6 12 6 6 6 6 6 6 6 6 6 6 6 6 6 4 5071 0.0023664
skin_tumor_A375 5 10 5 5 5 5 5 5 5 5 5 5 5 5 5 3 2264 0.0044170
Totals 824 475 440 440 439 439 438 438 435 433 432 431 428 426 422 418 24779 0.0332540

In a subset of cell lines, ligands were tested over a variety of doses and times (and EGF was especially rigorously assayed), while in most cell lines ligands were tested at a single concentration over two time points. Note that the number of control samples per cell type is much greater than the number of treatments.