Table 1.

Distribution of genes based on functional categories as categorized by mycobrowser.

Functional categories	Rx-1D				Rx-3D				Rx-5D				Rx-7D				Rx-14D
	Effective treatment		Ineffective treatment		Effective treatment		Ineffective treatment		Effective treatment		Ineffective treatment		Effective treatment		Ineffective treatment		Effective treatment		Ineffective treatment
	N	%	N	%	N	%	N	%	N	%	N	%	N	%	N	%	N	%	N	%
Cell wall and cell wall process	40	6	20	3	125	18	14	2	250	36	5	1	52	8	4	1	22	3	4	1
Conserved hypotheticals	76	7	26	3	126	12	20	2	400	39	5	0	48	5	4	0	30	3	2	0
Information pathways	15	7	14	6	41	18	15	7	78	34	4	2	18	8	0	0	11	5	5	2
Insertion sequences and phages	16	22	2	3	7	9	1	1	27	36	0	0	5	7	0	0	1	1	0	0
Intermediary metabolism and respiration	39	5	35	4	118	14	28	3	273	33	3	0	57	7	11	1	30	4	6	1
Lipid metabolism	10	4	19	8	48	21	14	6	30	13	7	3	25	11	2	1	18	8	2	1
Not classified	48	12	14	4	51	13	11	3	135	34	6	2	21	5	4	1	24	6	6	2
PE/PPE	12	8	10	6	21	13	11	7	72	46	0	0	16	10	3	2	8	5	1	1
Regulatory proteins	14	8	7	4	30	17	2	1	74	42	0	0	12	7	0	0	4	2	1	1
Virulence detoxification adaptation	14	14	4	4	22	22	4	4	38	38	0	0	12	12	0	0	8	8	1	1

N -Detected genes in each category, % percentage; numbers in bold represent the percentage of dysregulated gene calculated based on the number of genes in the particular functional category, numbers in italics indicate the significantly dysregulated functional categories. Rx-1d–Rx-14d – Days post-treatment initiation.