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. 2015 Jul 30;10(7):e0134595. doi: 10.1371/journal.pone.0134595

Table 2. Fold changes of genes differentially expressed after treatment with 0.2 mM and 7 mM H2O2 (treated vs untreated).

Gene Name Gene Product log2 Ratio (0.2mM/mc2155) P-value FDR log2 Ratio (7mM/mc2155) P-value FDR
DNA repair
msmeg_2839 transcriptional accessory protein -1.7523338 2.02E-243 5.7E-242 -1.6975845 9.0323E-80 5.4177E-79
alkA methylated-DNA—protein-cysteine methyltransferase -2.106759 8.54E-09 2.73E-08 -1.1090648 0.00020253 0.00030498
msmeg_1383 endonuclease IV -2.8849149 0 0 -0.4418784 0 0
msmeg_1756 endonuclease VIII and DNA N-glycosylase with an AP lyase activity 3.01822392 2.08E-105 3.04E-104 2.96577039 9.82E-104 7.22E-103
dnaE2 error-prone DNA polymerase 5.52502439 0 0 2.44964676 1.32E-277 2.48E-276
lig ATP-dependent DNA ligase 2.37386688 1.03E-184 2.21E-183 1.60677746 5.66E-69 3E-68
ligA NAD-dependent DNA ligase LigA 2.32734432 0 0 2.47575753 0 0
recA recombinase A 3.59091497 0 0 2.96402929 0 0
uvrB excinuclease ABC subunit B 3.25788081 0 0 4.50884994 0 0
lexA LexA repressor 3.10981267 0 0 1.01678782 4.81E-103 3.51E-102
radA DNA repair protein RadA 2.82617738 0 0 1.71244303 0 0
dinP DNA polymerase IV 4.26301055 1.85E-174 3.84E-173 4.18732816 2.79E-169 3.17E-168
msmeg_1622 putative DNA repair polymerase 4.79317887 8.44E-277 2.71E-275 -0.1339395 0.658812 0.69126208
recD exodeoxyribonuclease V, alpha subunit 3.50057135 3.24E-216 8.07E-215 2.03125644 2.04E-46 8.42E-46
msmeg_1756 endonuclease VIII and DNA N-glycosylase with an AP lyase activity 3.01822392 2.08E-105 3.04E-104 2.96577039 9.82E-104 7.22E-103
helicase ATP-dependent DNA helicase 4.16679804 0 0 4.74283172 0 0
tag DNA-3-methyladenine glycosylase I 2.81384991 2.09E-184 4.47E-183 2.86173411 2.34E-201 3.15E-200
Glycolysis/gluconeogenesis
msmeg_1543 eptc-inducible aldehyde dehydrogenase -2.6859775 8.91E-139 4.21E-148 -1.2892582 5.64E-56 2.60E-55
msmeg_1762 piperideine-6-carboxylic acid dehydrogenase 2.93235592 2.30E-149 4.21E-148 -1.6876011 2.28E-12 4.83E-12
pfkB 6-phosphofructokinase isozyme 2 -5.7653785 3.88E-196 8.90E-195 -2.8501465 6.61E-126 5.73E-125
pdhB pyruvate dehydrogenase E1 component subunit beta -3.2722769 3.01E-30 1.92E-29 0.71595693 5.59E-07 9.61E-07
pdhA pyruvate dehydrogenase E1 component, alpha subunit -3.4705711 1.84E-89 2.39E-88 -0.3895867 0.00010596 0.00016157
adhB alcohol dehydrogenase B -4.0478653 2.97E-105 4.33E-104 -2.1612025 4.92E-60 2.38E-59
msmeg_6616 S-(hydroxymethyl)glutathione dehydrogenase -2.956082 0.00E+00 0.00E+00 -1.1422205 1.36E-159 1.45E-158
msmeg_6687 aldehyde dehydrogenase, thermostable -3.706221 1.64E-29 1.03E-28 -1.5049935 9.36E-12 1.94E-11
msmeg_6834 alcohol dehydrogenase -2.7848309 2.21E-05 5.51E-05 0.08733237 0.840712 0.85579383
fadA acetyl-CoA acetyltransferase -2.7273404 0.00E+00 0.00E+00 0.33348045 5.36E-35 1.86E-34
fadB putative 3-hydroxyacyl-CoA dehydrogenase -2.6949142 0.00E+00 0.00E+00 1.39743214 0 0
msmeg_5199 putative acyl-CoA dehydrogenase -2.6174798 7.78E-91 1.02E-89 -0.4351779 5.88E-07 1.01E-06
msmeg_4832 acyl-CoA dehydrogenase -2.2726247 1.84E-34 1.30E-33 -1.4448556 2.45E-20 6.42E-20
msmeg_4833 putative acyl-CoA dehydrogenase -2.176661 8.50E-49 7.39E-48 -2.3488919 3.50E-57 1.65E-56
echA4 enoyl-CoA hydratase -2.5812975 1.27E-32 8.59E-32 -0.1876747 0.1805012 0.20801109
fadE13 putative acyl-CoA dehydrogenase -2.4369076 3.84E-11 1.38E-10 -0.1310912 0.579156 0.6139111
Sigma factors
sigG RNA polymerase factor sigma-70 2.93398738 0 0 3.88123043 0 0
msmeg_0573 putative ECG sigma factor RpoE1 1.38509413 0.0569946 0.08901435 7.09387521 1.35E-209 1.91E-208
msmeg_0574 putative ECG sigma factor RpoE1 0.18840222 0.422278 0.5067336 4.08443636 3.1E-276 5.78E-275
msmeg_1348 RNA polymerase ECF-subfamily protein sigma factor -0.0465176 0.804554 0.84797939 -2.3586787 1E-17 2.48E-17
sigL RNA polymerase sigma factor SigL 0.52825986 0.00083713 0.00176811 -2.2355973 4.27E-20 1.12E-19
msmeg_1970 sigma factor -1.6126499 4.2715E-20 1.1152E-19 -4.1999183 4.27E-20 1.12E-19
mysB RNA polymerase sigma factor SigB -0.4921846 4.74E-104 6.85E-103 2.50111799 0 0
msmeg_3008 putative sigma 54 type regulator -1.8964762 1.61E-11 5.87E-11 -2.0197975 3.44E-13 7.46E-13
msmeg_5214 RNA polymerase sigma-70 factor 4.65312922 2.09E-184 4.47E-183 2.81376729 1.63E-13 3.59E-13
msmeg_5444 RNA polymerase sigma-70 factor protein 0.03717083 0.894318 0.91679688 -2.0919913 9.72E-09 1.8E-08
Transcriptional Regulators
devR two-component system response regulator 1.01514452 0.00136283 0.00280756 6.64431111 0 0
furA (msmeg_6383) transcription regulator FurA 2.0393827 1.57E-38 1.19E-37 4.16725591 0 0
phoP DNA-binding response regulator PhoP 2.90191537 4.67E-220 1.19E-218 -0.5325639 0.00089158 0.00128064
msmeg_4517 TetR-type transcriptional regulator of sulfur metabolism 3.21516913 0.00000169 0.00000457 4.13040109 7.31E-14 1.62E-13
msmeg_4925 transcriptional regulator 0.69321643 0.00330216 0.00644626 2.93688979 1.02E-78 6.03E-78
msmeg_1919 Transcription factor WhiB 2.52297686 0 0 1.07820136 2.53E-126 2.21E-125
msmeg_4025 transcriptional regulator, LysR family protein 1.30263197 0.00055968 0.00120459 5.38130323 1.6E-210 2.28E-209
msmeg_6253 fur family protein transcriptional regulator 1.24070422 0.0469844 0.07479434 3.90800867 1.22E-25 3.59E-25
Detoxification enzymes
trxB thioredoxin-disulfide reductase -0.0780198 0.1478068 0.20755437 2.71109242 0 0
trx thioredoxin 0.12205973 0.0602136 0.09347541 3.84889994 0 0
msmeg_6884 NADP oxidoreductase 0.87052096 0.1166366 0.1680318 4.68101209 4.52E-68 2.38E-67
KatG catalase/peroxidase HPI 3.82587233 0 0 4.95397834 0 0
msmeg_4890 alkylhydroperoxidase 3.42735043 6.73E-19 3.21E-18 4.22476909 0.0465926 0.05777446
msmeg_3448 two-component system sensor kinase 0.55015338 0.1588256 0.22100457 5.07235098 4.09E-202 5.55E-201
ahpD alkylhydroperoxidase AhpD core -2.3697934 0.0210456 0.03618406 3.85029317 4.71E-31 1.53E-30
msmeg_3708 catalase 2.47422002 5.45E-56 5.11E-55 -3.0001305 5.73E-15 1.31E-14