Table 2.
Genes that when knocked down sensitized multiple cell lines to drugs. Threshold analysis provides a set of target genes based on strict statistical criteria. Rank order analysis provides a different view of the target gene set by compensating for stochastic noise in the responsiveness of cell lines (including DLD-1, DKS-8, LoVO, MIA PaCa-2, Panc1, and HCT116) with nonspecific drug-resistance mutations, such as in the genes encoding K-RAS or p53. For rank analysis, genes indicated represent those found in the highest and lowest quartiles based on absolute activity for each of the categories specified.
Cutoff Analysis Only | Rank Analysis Only | |
---|---|---|
Genes that sensitize A431 cells to erlotinib and cetuximab | ASCL2 CDH3 CXCL12 DIXDC1 DLG4 DUSP7 FLNA INPPL1 PLSCR1 PPIAP19 PRKACB PRKCE PRKCZ RPS6KA5 SC4MOL SH2D3C |
CDH3 CXCL12 FLNA INPPL1 PRKACB PRKCE RPS6KA5 SC4MOL SH2D3C |
Genes that sensitize two or more cell lines to erlotinib | AKT2 ASCL2 BCAR1 CD59 DIXDC1 DUSP7 FLNA LTK PIK3R2 PRKACB PRKCD PRKCE RPS6KA5 SC4MOL SH2D3C |
AKT2 ASCL2 BCAR1 CD59 DIXDC1 DLG4 DUSP7 FLNA KLF10 LTK NEDD9 PRKACB PRKCE SC4MOL SH2D3C SHC1 |
Genes that sensitize one or more resistant cell lines to erlotinib | AKT2 BCAR1 CD59 DIXDC1 DUSP7 EPHA5 NEDD9 PIK3R2 PRKACB SC4MOL SH2D3C SHC1 |
AKT2 ANXA6 ASCL2 BCAR1 CD59 DIXDC1 DLG4 DUSP6 DUSP7 EPHA5 FGFR2 KLF10 LOC63920 LTK NEDD9 PKN2 PPIAP19 PRKACB RET SC4MOL SH2D3C SHC1 |
Genes that sensitized cells to both erlotinib and CPT11 in >3 cell lines, | none | BCAR1 CD59 DLG4 |
Genes that sensitized cells to erlotinib and CPT11, but did not reduce viability in the absence of drug | CXCL12 (only in A431) | DLG4 DUSP6 |
Genes that affected both the viability and sensitization to erlotinib or CPT11 in ≥ 2 tumor cells lines | ASCL2 BCAR1 DUSP7 ERBB3 FLNA INPPL1 LTK PIK3R2 PRKACB PRKCD PRKCE RASA3 RPS6KA5 SC4MOL SH2D3C SHC1 SOS2 VAV3 |
DIXDC1 FLNA PRKCE SH2D3C SHC1 |
Genes that reduced viability of at least 2 RAS mutant cell lines but not more than one wild-type cell line | AKT2 ARF4 CDH3 CXCL12 DUSP7 FLNA LOC63920 PPIAP19 |
ANXA6 FLNA PPIAP19 |