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. 2016 Jun 30;6:28985. doi: 10.1038/srep28985

Table 3. Differential proteins identified on the gene regulatory network.

Synonym Gene Reg TF Product Functional_category log2 fold p-value
Rv0509 – over Rv1353c glutamyl-tRNA reductase Intermediary metabolism and respiration    
Rv1464 – over Rv1460 cysteine desulfurase Intermediary metabolism and respiration 1.56 0.0489072
Rv3094c fadE2 over Rv0494; Rv3095 hypothetical protein Intermediary metabolism and respiration 9.61 0.0386941
Rv3494c yrbE1A over Rv0022c Mce family protein Mce4 virulence, detoxification, adaptation 1.46 0.0259927
Rv3570c mce1A over Rv0678; Rv1353c; Rv3574 flavin-dependent monooxygenase oxygenase subunit HsaA Intermediary metabolism and respiration 1 0.0438151
Rv0034 – under Rv3249c hypothetical protein Intermediary metabolism and respiration    
Rv0035 – under Rv3249c fatty-acid–CoA ligase FadD34 Lipid metabolism    
Rv0081 bioF2 under Rv0081 HTH-type transcriptional regulator Regulatory proteins    
Rv0087 acpA under Rv0081 formate hydrogenase HycE Intermediary metabolism and respiration    
Rv0101 – under Rv0047c; Rv2069; Rv0324 peptide synthetase Nrp Lipid metabolism    
Rv0154c fadD34 under Rv1423 acyl-CoA dehydrogenase FadE2 Lipid metabolism −0.59 0.0008057
Rv0169 – under Rv0023; Rv0081; Rv0757; Rv1049; Rv3416 Mce family protein Mce1A virulence, detoxification, adaptation −1.44 5.763E-06
Rv0170 – under Rv0023; Rv0081; Rv1049; Rv3416 Mce family protein Mce1B virulence, detoxification, adaptation −1.38 0.0017153
Rv0172 sdaA under Rv0023; Rv0081; Rv1049 Mce family protein Mce1D virulence, detoxification, adaptation −1.38 0.0001941
Rv0173 glyA2 under Rv1049 Mce family lipoprotein LprK cell wall and cell processes −1.29 7.012E-05
Rv0174 - under Rv0023; Rv0081; Rv1049 Mce family protein Mce1F virulence, detoxification, adaptation −0.84 7.012E-05
Rv0176 – under Rv1049 Mce associated transmembrane protein cell wall and cell processes −1.81 0.0175553
Rv0241c – under Rv0238; Rv1049 3-hydroxyacyl-thioester dehydratase HtdX Intermediary metabolism and respiration −0.86 0.0386941
Rv0243 – under Rv0238 acetyl-CoA acetyltransferase FadA Lipid metabolism −0.91 0.0166606
Rv0675 – under Rv0674 enoyl-CoA hydratase EchA5 Lipid metabolism −1.1 0.0007597
Rv0768 – under Rv0576; Rv1255c aldehyde dehydrogenase AldA Intermediary metabolism and respiration    
Rv0824c hycD under Rv0472c acyl-ACP desaturase DesA Lipid metabolism −1.98 5.763E-06
Rv0989c hycP under Rv0767c polyprenyl-diphosphate synthase GrcC Intermediary metabolism and respiration    
Rv1094 hycQ under Rv0472c acyl-ACP desaturase DesA Lipid metabolism −1.91 5.196E-09
Rv1192 hycE under Rv2034; Rv0081 hypothetical protein cell wall and cell processes −1.91 0.0006327
Rv1386 - under Rv1033c; Rv2359 PE family protein PE15 PE/PPE    
Rv1856c fcoT under Rv1353c oxidoreductase Intermediary metabolism and respiration −1.06 0.037951
Rv1997 ctpF under Rv3133c cation transporter ATPase F cell wall and cell processes    
Rv2004c – under Rv3133c hypothetical protein Regulatory proteins −1.45 0.0004367
Rv2005c nrp under Rv3133c universal stress protein virulence, detoxification, adaptation −1.24 0.023446
Rv2029c gmhB under Rv3133c 6-phosphofructokinase PfkB Intermediary metabolism and respiration −3 0.0006327
Rv2048c hddA under Rv0767c polyketide synthase Lipid metabolism −1.38 0.0393413
Rv2103c msrA under Rv1990c ribonuclease VapC37 virulence, detoxification, adaptation    
Rv2410c – under Rv0022c hypothetical protein Intermediary metabolism and respiration −1.42 0.0082996
Rv2623 – under Rv3133c universal stress protein virulence, detoxification, adaptation −1.26 0.0157466
Rv2626c ptbB under Rv3133c hypoxic response protein Regulatory proteins −1.56 0.0216908
Rv3130c pntAa under Rv3133c diacyglycerol O-acyltransferase Lipid metabolism −2.29 0.0001161
Rv3131 pntAb under Rv3133c NAD(P)H nitroreductase Intermediary metabolism and respiration −1.69 0.0026414
Rv3400 pntB under Rv0135c hydrolase Intermediary metabolism and respiration −0.93 0.0451627
Rv3509c yrbE1B under Rv0324 acetohydroxyacid synthase large subunit Intermediary metabolism and respiration −0.66 0.0080181
Rv3602c mce1B under Rv1353c pantothenate synthetase Intermediary metabolism and respiration −1.25 0.0014439
Rv3825c mce1C under Rv0757 phthioceranic/hydroxyphthioceranic acid synthase Lipid metabolism −1 0.0316068