TABLE 5.

MOA classification of antibiotics and underexpression effects in conditional mutants based on whole-genome expression profiles^a

Compound or mutantb	Predefined MOA class	MOA classifier affinity value				MOA assignment
		DNA	Protein	Cell wall	AATS-FAB
AZA	DNA	1.561	−1.569	0.1021	0.25	DNA
NAL	DNA	1.441	−1.292	−0.6124	0.6667	DNA
CIP	DNA	1.321	−0.3693	0.1021	−0.6667	DNA
ACT	Protein	0.5103	1.837	0.4082	−2.25	Protein
GEN	Protein	0.1021	1.837	0.8165	−2.25	Protein
CHL	Protein	−0.3062	1.837	−0.1021	−1.167	Protein
AZI	Protein	0.5103	1.837	0.2041	−2.083	Protein
OXA	Cell wall	0.2041	−1.477	1.561	0.08333	Cell wall
MET	Cell wall	−0.9186	−1.108	1.561	0.6667	Cell wall
VAN	Cell wall	−1.021	−1.477	1.321	1.25	Cell wall
CER	AATS-FAB	0.2752	−1.9	0.8257	0.9	AATS-FAB
FABF(−)	AATS-FAB	−0.6055	−1.7	0.2752	2	AATS-FAB
MUP	AATS-FAB	−0.3853	−2	0.3853	2	AATS-FAB
ILES(−)	AATS-FAB	−0.3853	−2	0.4954	1.9	AATS-FAB
PTU	AATS-FAB	−0.1651	−2	0.3853	1.8	AATS-FAB
PHEST(−)	AATS-FAB	0.05505	−1.9	0.05505	1.8	AATS-FAB
MOIB	?	−0.80861	−1.97	0.42809	2.07	AATS-FAB
ACCDA(−)	?	−0.61835	−1.2	0.1427	1.46	AATS-FAB

^aThirteen compounds and three mutants were preassigned to MOA classes based on a priori biological knowledge. Five global MOA classes were differentiated: DNA, DNA synthesis; Protein, protein synthesis; Cell wall, cell wall biosynthesis; and FAB-AATS, aminoacyl-tRNA synthesis-fatty acid biosynthesis. This compound MOA preassignment was cross-validated by taking out the profiles for each compound or compound-mutant pair (leave-one-out strategy) and subsequently reclassifying their profile(s) based on the remaining N-1 (N-2) compound profiles (see Materials and Methods). The affinity values represent the output of the Wilcoxon MOA classifier (Expressionist; Genedata). The compounds and mutants were automatically assigned to the MOA class for which the highest affinity value was calculated (boldface). The predicted MOA assignments are summarized. The results show an overall consistent picture, meaning that the reference compendium data are consistent with regard to the microarray data quality and the a priori MOA classification. For instance, the recently characterized PheST inhibitor PTU was indeed correctly assigned to the FAB-AATS class. Of particular importance is that the conditional mutants are correctly classified in their respective target classes. The results also indicate that the so-far-uncharacterized compound MOIB is acting via a previously unknown MOA. It is classified into the same FAB-AATS category as the mutant ACCDA(−) on the basis of the cross-validated reference compendium (last two rows).

^bSee Table 2 for definitions of drug abbreviations.