Table 2 Data sources used in the study.
Data source | Dataset name | Data type | Drug | Treatment time | Drug concentration | Number of cell lines | Cell Lines and tissue type |
|---|---|---|---|---|---|---|---|
iLINCS Data Portal | Pharmacogenomics transcriptional signatures | Drug perturbation-associated gene expression | Bortezomib | 2, 6, 24 h | 10 and 100 nM | 60 | Breast (BT-549, HS-578 T, MCF7, MDA-MB-231, MDA-MB-435, MDA-MB-468, T-47D), CNS (SF-268, SF-295, SF-539, SNB-19, SNB-75, U251), Colon (COLO-205, HCC-2998, HCT-15, KM12, SW-620), Large intestine (HT29), Large intestine epithelial (HCT-116), Leukemia (CCRF-CEM, HL-60, K-562, MOLT-4, RPMI-8226, SR), Lung (A549, EKVX, HOP-62, HOP-92, NCI-H226, NCI-H23, NCI-H322M, NCI-H460, NCI-H522), Melanoma (LOX, M14, MALME-3 M, SK-MEL-2, SK-MEL-28, MEL-5, UACC-257, UACC-62), Ovarian (IGR-OV1, NCI-ADR-RES, OVCAR-3, OVCAR-4, OVCAR-5, OVCAR-8, SK-OV-3), Prostate (DU-145, PC-3), Renal (786-0, A498, ACHN, CAKI-1, RXF-393, SN12C, TK-10, UO-31) |
Connectivity Map (CMap) | Drug perturbation-associated gene expression | MG-132 | 6 and 24 h | 1, 10, 100, 500 nM; 1, 3, 10 µM | 16 | Adipose stroma (ASC), Breast (MCF7, SKB), CNS (NEU), Colorectal (HT29), Liver (HEPG2, PHH), Lung (A549, HCC515), Melanoma (A375), Nasopharyngeal (NPC), Pluripotent stem cell (FIBRNPC), Prostate (PC3, VCAP), Renal (HA1E, NKDBA) | |
Drug perturbation-associated gene expression | MLN-2238 | 6 and 24 h | 500 nM; 1, 3, 10 µM | 51 | Breast (MCF7), Colon (CL34, HCT116, HT115, RKO, SW480, SW948), Colorectal (HT29, LOVO, MDST8, SNUC4, SNUC5, SW620), Endometrium (HEC108, SNGM), Large intestine (NCIH508, SNU1040), Leukemia (NOMO1, PL21, SKM1, THP1, U937), Liver (HEPG2), Lung (A549, CORL23, DV90, H1299, HCC15, HCC515, NCIH1694, NCIH1836, NCIH2073, NCIH596, SKLU1, T3M10), Lymphoma (WSUDLCL2), Melanoma (A375, SKMEL1, SKMEL28), Ovarian (COV644, EFO27, OV7, RMGI, RMUGS, TYKNU), Prostate (PC3, VCAP), Renal (HA1E, NKDBA), Soft tissue (A673), Stomach (AGS), Uterine-cervix (JHUEM2) | ||
Drug perturbation similarity | MG-132 | 9 | Breast (MCF7), Colorectal (HT29), Liver (HEPG2), Lung (A549, HCC515), Melanoma (A375), Prostate (PC3, VCAP), Renal (HA1E) | ||||
Drug perturbation similarity | MLN-2238 | ||||||
L1000 fireworks display (L1000FWD) | Drug perturbation similiarity |
