Table 1.

Genes selected by the shEnrich method

shEnrich Method
Forward shEnrich
shRNA family size 2DDR2PPP5C*
PPP2R1ADKFZP566K0524PRG-3
PTBP1*DUSP13PRKWNK3
RIOK2EAT2PTPRM*
shRNA family size 3EEF2K*RAF1*
CDC25A*EIF2AK3RIMS4
PTPN18EPM2ASGPP2
TP53RKFBP2SH2D1A*
shRNA family size 4FLJ25449SMG1*
BLK*Gpr109bSNRK*
CKMGUCY2CSPAP1
DUSP5*IMPA2SYT14L
EGLN1*INPP5FWWP2*
FLJ16518IRAK1*shRNA family size 8
GALK2ITPKACIB2
GMFBLOC283871ERBB4*
HYPBLOC401313
INPP5BLPPR4
KIAA2002MAP3K11*Reverse shEnrich
LOC400687MAP3K7IP1shRNA family size 2
LOC441868MAPK4CALM1*
LOC90353NR1I3*PPP2R1A*
LOC91461NT5EDUSP9
NEK7NUDT11shRNA family size 3
NUDT10OBSCN*PPAP2A
PHKA2*PCTK3SSH3
PIN1*PIB5PAshRNA family size 4
PMVKPIP5K1AGPR109A
PTPN22*PLCB4LCK*
PTPN5PPAPDC1PPP1R14D
PTPREPPAPDC1ASIK2*
RIPK5PPEF1*TRPV5*
RXRBPPEF2*shRNA family size 5
SACM1LPPFIA1*CDC14A*
TEX14PPM1JENPP1
TRPM7*PPP1R12B*EPB41L4A
shRNA family size 5PPP2CB*NME5
ABL1*PPP3CA*PIM1*
AKAP11*PPP4R1*PKIB
CKS2*PPP4R1LPRKCA*
  • NOTE: The shEnrich method selected genes that had consistent shRNA effects in the forward direction (shRNAs increased TPA-induced TGFα shedding) and in the reverse direction (shRNAs decreased TPA-induced TGFα shedding). Asterisks indicate genes that are included in following network analysis.