#warning windows double quotes
perl -lanE "print $F[0],qq(\t)x($F[3]=~/Pro/?1:$F[3]=~/Bact/?2:3),$F[4]" genetable.txt

ENSG00000088992 0.31
ENSG00000105374 0.37
ENSG00000005810         0.29
ENSG00000088992         0.27
ENSG00000109016         -0.37
ENSG00000069248         0.32
ENSG00000005810                 -0.29
ENSG00000105374                 -0.27
ENSG00000105374                 -0.27
ENSG00000105374                 -0.30
ENSG00000133107         0.35