Table 1.

Genes induced in wild-type M. avium subsp. paratuberculosis, relative to the levels for the M. avium subsp. paratuberculosis ΔsigH mutant following diamide exposure^a

Functional classification	Geneb	Fold expression	FDR P value correction	Old locus tagc	M. tuberculosis ortholog	Protein similarity (%)
Chaperone/protein turnover	hsp	11.01	0.00	MAP3701c	Rv0251c	78.61
	dnaJ2	3.57	0.00	MAP2162c	Rv2373c	84.81
	clpB	3.49	0.00	MAP3853	Rv0384c	91.98
	hflX	7.01	0.00	MAP2839c	Rv2725c	82.88
	clpC	4.54	0.00	MAP0461	Rv3596c	92.38
	MAPK_2184	2.53	0.00	MAP1584c	Rv2897c	44.96
Oxidative stress scavenger/detoxification	trxB2	3.77	0.00	MAP4339	Rv3913	77.5
	trxC	2.89	0.00	MAP4340	Rv3914	94.82
	ephA	3.06	0.00	MAP0446c	Rv3617	85.89
	adhE	4.71	0.00	MAP3596c	Rv0162c	67.31
	adhB	2.51	0.00	MAP0595c	Rv0761c	94.66
	aldB	3.72	0.00	MAP3413	Rv3293	79.79
Regulatory/transcription	MAPK_0206	8.46	0.00	MAP3562	Rv0144	76.77
	MAPK_1421	5.25	0.00	MAP2347	Rv3060c	40.61
	whiB4	5.14	0.00	MAP0393	Rv3681c	96.87
	MAPK_0357	4.76	0.00	MAP3411c	Rv3291c	92
	MAPK_0097	3.95	0.00	MAP3671	Rv0232	73.36
	MAPK_1985	3.32	0.00	MAP1783	Rv0067c	45.86
	MAPK_0788	3.08	0.00	MAP2980c	Rv2912c	87.69
	whiB2	3.04	0.00	MAP3372c	Rv3260c	98.59
	MAPK_3589	2.87	0.00	MAP0179c	Rv3855	73.48
	MAPK_1209	2.84	0.00	MAP2559	Rv1219c	89.95
	MAPK_1920	2.75	0.01	MAP1848c	Rv3830c	44.38
	MAPK_4083	2.75	0.02	MAP4081	Rv0586	76.39
	MAPK_3159	2.62	0.01	MAP0609	Rv0775	81.77
	MAPK_0193	2.52	0.00	MAP3575	Rv0158	93.8
	sigH	5.60	0.00	MAP3324c	Rv3223c	90.9
	sigE	5.04	0.00	MAP2557c	Rv1221	88.42
	sigB	3.5	0.00	MAP2826	Rv2710	98.12
	sigD	2.94	0.00	MAP4275	Rv3414c	78.28
Two-component system	MAPK_2766	9.89	0.00	MAP1002c	Rv1033c	85.21
	MAPK_2767	6.34	0.00	MAP1001c	Rv1032c	65.46
	mtrA	3.70	0.00	MAP3360c	Rv3246c	87.28
	MAPK_2852	3.17	0.00	MAP0916	Rv0981	91.66
	senX3	2.51	0.00	MAP3982	Rv0490	82.68
Virulence	MAPK_0165	5.01	0.00	MAP3603	Rv0168	66.53
	MAPK_1919	4.95	0.00	MAP1849	Rv0587	59.9
	mceA1	3.79	0.00	MAP3604	Rv0169	77.3
	MAPK_1913	3.76	0.00	MAP1855	Rv0593	48.19
	MAPK_0166	3.71	0.00	MAP3602	Rv0587	89.18
	MAPK_1918	3.66	0.00	MAP1850	Rv3500c	50.72
	mceC	3.02	0.00	MAP3606	Rv0171	87.47
	MAPK_2565	2.96	0.00	MAP1203	Rv1477	73.31
	mce5A	2.94	0.03	MAP1851	Rv3494c	44.97
	mceB2	2.81	0.00	MAP3605	Rv0170	89.59
	MAPK_1916	2.80	0.02	MAP1852	Rv1967	54.33
	MAPK_1914	2.59	0.04	MAP1854	Rv3496c	50.17
	mceD	2.52	0.00	MAP3607	Rv0172	82.78
Central intermediary/sulfate metabolism	ppdK	2.93	0.00	MAP2664	Rv1127c	76.79
	rmlB	5.32	0.00	MAP4225c	Rv3464	95.46
	rmlC	4.18	0.00	MAP4224c	Rv3465	89.28
	MAPK_1169	10.79	0.00	MAP2599c	Rv1286	62.76
	cysQ_2	2.81	0.00	MAP2058c	Rv2131c	69.33
	cysD	2.52	0.00	MAP2485c	Rv1285	82.37
Energy metabolism	icl	2.57	0.05	MAP3961	Rv0467	97.36
	rpi	6.53	0.00	MAP2285c	Rv2465c	96.17
	tpi	6.44	0.00	MAP1166	Rv1438	91.57
	ccsB	7.10	0.00	MAP4025	Rv0529	76.92
	nuoA	4.95	0.00	MAP3201	Rv3145	73.43
	nuoB	3.95	0.00	MAP3202	Rv3146	91.3
	nuoD	3.66	0.00	MAP3204	Rv3148	95.21
	nuoC	3.57	0.00	MAP3203	Rv3147	86.01
Cell envelope associated	mmpL4_1	4.60	0.00	MAP0076	Rv0402c	68.15
	MAPK_4322	4.10	0.00	MAP4320	Rv0402c	53.19
	mmpS3	4.02	0.00	MAP1938c	Rv2198c	98.88
	MAPK_3948	3.16	0.00	MAP3946	Rv0677c	50.33
	mmpS4	2.78	0.00	MAP1241c	Rv0451c	73.52
	lpqD	3.39	0.00	MAP3481	Rv3390	77.02
	MAPK_0832	2.95	0.00	MAP2936c	Rv2864c	89.72
Cell processes/transport	MAPK_3150	2.66	0.00	MAP0618c	Rv0783c	70.65
	efpA_2	2.60	0.00	MAP2915c	Rv2846c	79.92
	MAPK_4062	4.28	0.00	MAP4060c	Rv3273	64.47
	fdxC_2	9.70	0.00	MAP2607c	Rv1177	96.22

^aThe functional categorization of M. avium subsp. paratuberculosis genes was based on their known functions as assigned in the Integrated Microbial Genomes system (http://http://img.jgi.doe.gov).

^bImproved annotations according to the revised genome sequence of M. avium subsp. paratuberculosis (35).

^cAnnotations according to Li et al. (32).