TABLE 2 .
Gene tag | Gene name |
Functional categorya |
Function (reference) | RPKM ratiob |
P valuec |
||
---|---|---|---|---|---|---|---|
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 TCSe | — | 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 |
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.
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.
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).
—, gene with a ratio of <1 or with no significantly increased expression under those conditions.
TCS, two-component regulatory system.