. 2014 May 20;5(3):e01125-14. doi: 10.1128/mBio.01125-14

TABLE 2 .

Member genes of the dormancy regulon with significantly increased expression in the fatty acid model

Gene tag	Gene name	Functional category^a	Function (reference)	RPKM ratio^b		P value^c
Gene tag	Gene name	Functional category^a	Function (reference)	FE/DE	FS/DS	FE vs DE	FS vs DS
Rv0079		10	Unknown; probable transduction regulatory protein (42)	1.59	2.10	1.09 E-12	3.37 E-07
Rv0080		10		—^d	9.00	—	1.19 E-09
Rv0081		9	Global regulator in hypoxia	—	1.10	—	0.014
Rv0243	fadA2	1	Lipid degradation	—	1.60	—	9.87 E-05
Rv0569		10		—	3.07	—	0.90 E-14
Rv0570	nrdZ	2	Ribonucleoside-diphosphate reductase	—	2.67	—	0.004
Rv1436	gap	7		1.15	—	0.028	—
Rv1652	argC	7	Arginine biosynthesis	—	3.00	—	8.33 E-05
Rv1733c		3	Unknown; probable conserved transmembrane protein	2.77	1.50	2.62 E-08	0.012
Rv1738		10		—	1.15	—	0.90 E-14
Rv1813c		10		3.53	—	1.09 E-12	—
Rv1996		0	Unknown; universal stress family protein	1.93	1.19	1.09 E-12	6.27 E-06
Rv2005c		0	Unknown; universal stress family protein	—	6.50	—	3.15 E-13
Rv2007c	fdxA	7	Ferredoxin FdxA	—	2,18	—	1.09 E-12
Rv2030c		10		—	5.25	—	3.88 E-10
Rv2031c	hspX	0	Stress protein induced in hypoxia	—	6.05	—	0.90 E-14
Rv2623	TB31.7	0	Unknown; universal stress family protein	—	3.08	—	0.90 E-14
Rv2625c		3	Unknown; probable conserved transmembrane protein	—	3.20	—	1.44 E-06
Rv2626c	hrp-1	10		—	4.67	—	0.90 E-14
Rv2627c		10		—	2.43	—	2.96 E-06
Rv2628		10		—	1.40	—	1.18 E-05
Rv2629		10		—	1.13	—	4.16 E-08
Rv3127		10		—	1.33	—	0.003
Rv3130c	tgs-1	1	TAG	—	2.31	—	2.07 E-13
Rv3131		10	Unknown; putative NAD(P)H nitroreductase	2.89	4.00	1.09 E-12	9.04 E-13
Rv3133c	devR	9	Regulator part of the Dos TCS^e	—	2.60	—	6.54 E-05
Rv3134c		0	Unknown; universal stress protein family	1.03	3.43	5.99 E-06	3.19 E-10

^{^a}

Functional categories based on http://www.tuberculist.epfl.ch: 0, virulence, detoxification, and adaptation; 1, lipid metabolism; 2, information pathways; 3, cell wall and cell processes; 7, intermediary metabolism and respiration; 9, regulatory proteins; 10, conserved hypothetical proteins.

^{^b}

RPKM ratio according to phase of growth: exponential (FE/DE) or stationary (FS/DS). See Table S1A and B in the supplemental material for the complete set of data. The gene is overexpressed in FE or FS if the ratio is above 1.

^{^c}

Determined by Fisher exact test, in which statistically significant differential expression between two conditions was determined by looking at genes with FDRs of <0.05 (see Materials and Methods for details).

^{^d}

—, gene with a ratio of <1 or with no significantly increased expression under those conditions.

^{^e}

TCS, two-component regulatory system.