Table 1.
Gene sets and top genes varying in concert with PT.
| Cell Line | Top Gene Sets Changing with PT | Top-10 Genes | ||
|---|---|---|---|---|
| BRAF/NRAS | Correlated | Anti-Correlated | Correlated | Anti-Correlated |
| wt/wt | Sister chromatid cohesion (10−11) 1 |
Cell adhesion (10−10) | H2AFZ CHCHD6 CD63 TRPM1 MLANA GSTP1 TUBA1B SLC25A5 HSPD1 PMEL (<10−8) |
ANXA1 CALD1 (<10−5) LIMA1 CRYAB FN1 ANXA2 ABL2 FKBP9 A2M ARID5B (<0.002) |
| Chromosome, centromeric region (10−11) |
Ras guanyl-nucleotide exchange factor activity (10−10) | |||
| DNA replication (10−11) | Extracellular matrix organization (10−9) |
|||
| Kinetochore (10−11) | Proteinaceous extracellular matrix (10−9) |
|||
| Cell division (10−10) | Skeletal muscle tissue development (10−9) | |||
| mut/wt | Mitochondrial inner membrane (0.008) | Extracellular matrix organization (0.008) |
UQCRHL UQCRH MRPL24 (<0.07) FIBP CCDC167 RAB18 CYC1 KPNA2 RBMX RAB32 (<0.14) |
EIF4G3 TUBG1 MITD1 TRIB2 (<0.2) SESN1 TSN EXO1 BIRC5 ITGAE SKA2 (<0.3) |
| Mitochondrial respiratory chain complex I assembly (0.01) | Collagen trimer (0.01) | |||
| Mitochondrion (0.01) | Negative regulation of cell adhesion (0.01) |
|||
| Chromatin (0.01) | Ras guanyl-nucleotide exchange factor activity (0.02) |
|||
| DNA metabolic process (0.01) |
Cell adhesion (0.02) | |||
| Cell division (0.01) | ||||
| wt/mut | DNA replication (10−10) | Calcium ion binding (10−6) | RAD51AP1 PRIM1 (<10−5) KNTC1 NUP107 BARD1 RRM2 CDK1 HAT1 DEK HELLS (<0.001) |
GIGYF2 SORBS2 TANC1 (0.02) SLITRK6 STAT2 (0.03) PTPRS FUNDC2 TMX2 LOXL3 TM9SF2 (0.05) |
| Cell division (10−9) | Carbohydrate binding (10−5) | |||
| Mitotic nuclear division (10−9) |
Endoplasmic reticulum lumen (10−5) |
|||
| Sister chromatid cohesion (10−9) |
Extracellular region (10−5) | |||
| Mitotic sister chromatid segregation (10−9) | Golgi membrane (10−5) | |||
1 False discovery rate (fdr) using likelihood ratio test.