GENES 2867:::H37Ra..7H9.roll.replicate.4 2867:::H37Ra..Dubos.media.replicate.2 2867:::H37Ra..Dubos.media.replicate.3 2885:::H37Rv..7H9.roll.replicate.4 2885:::Strain.1006...replicate.4 2885:::Strain.CDC1551..replicate.4 4060:::H37Rv.0.05..SDS.exposure.for.1h.rep.2 4060:::H37Rv.0.05..SDS.exposure.for.1h.rep.4 4060:::H37Rv.0.05..SDS.exposure.for.1h.rep.6 4060:::H37Rv.wild.type.Vs.H37Rv.sigE.null.mutant.rep.1 4062:::H37Rv.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.2 4062:::H37Rv.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.5 4062:::MTB.strain.1254.Ctrl.vs.0.05.mM.DETA.NO.40min.rep.7 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.16hrs.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.16hrs.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.16hrs.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.16hrs.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.1hr.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.1hr.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.1hr.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs...0.5.mM.DNO.40min.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.24hrs.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.2hrs.rep.4 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.40min.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.DETA.NO.8hrs.rep.3 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN...2hr.hypoxia.rep.2 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.1hr.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.20min...0.05.mM.DETA.NO.40min.rep.1 4062:::MTB.strain.1254.Ctrl.vs.0.5.mM.KCN.20min...0.05.mM.DETA.NO.40min.rep.2 4062:::MTB.strain.1254.Ctrl.vs.2hr.Hypoxia.rep.2 4062:::MTB.strain.1254.Ctrl.vs.high.aeration...0.01.mM.DETA.NO.rep.1 4062:::MTB.strain.1254.Ctrl.vs.high.aeration...0.01.mM.DETA.NO.rep.3 4062:::MTB.strain.1254.Ctrl.vs.high.aeration.rep1 4062:::MTB.strain.1254.Ctrl.vs.high.aeration.rep2 4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.005.mM.DETA.NO.rep.1 4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.005.mM.DETA.NO.rep.3 4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.05.mM.DETA.NO.rep.1 4062:::MTB.strain.1254.Ctrl.vs.low.aeration...0.05.mM.DETA.NO.rep.2 4062:::MTB.strain.1254.Ctrl.vs.low.aeration..0.2..oxygen..2hr.rep.2 4062:::MTB1254.Day.0.rep.2 4062:::MTB1254.Day.0.vs.low.Oxygen.Day.4.rep.5 4062:::MTB1254.Day.0.vs.low.Oxygen.Day.4.rep.6 4068:::H37Rv.SDS.treated.vs..H37Rv.delta.mprAB.mutant.SDS.treated.rep.6 4089:::H37Rv.wild.type.vs..H37Rv.whiB7.null.rep.1 4089:::MTB1254.control.vs..0.5.ug.ml.Streptomycin.for.15.min.rep.3 4089:::MTB1254.control.vs..0.5.ug.ml.Streptomycin.for.15.min.rep.5 4089:::MTB1254.control.vs..100.ug.ml.Streptomycin.for.15.min.rep.1 4089:::MTB1254.control.vs..100.ug.ml.Streptomycin.for.15.min.rep.4 4089:::MTB1254.ethanol.vs..0.5.ug.ml.Erythromycin.for.15.min.rep.4 4089:::MTB1254.ethanol.vs..0.5.ug.ml.Tetracyclin.for.30.min.rep.1 4089:::MTB1254.ethanol.vs..0.5.ug.ml.Tetracyclin.for.30.min.rep.3 4089:::MTB1254.ethanol.vs..5.0.ug.ml.Erythromycin.for.30.min.rep.1 4089:::MTB1254.ethanol.vs..5.0.ug.ml.Tetracyclin.for.15.min.rep.4 4099:::H37.Rv3133c.DosR.mutant.2hr.rep.3 4099:::H37Rv.hypoxia.2hr.rep.1 4099:::H37Rv.hypoxia.2hr.rep.2 4101:::H37Rv.Day.0.vs.low.Oxygen.Day.4.rep.1 4101:::H37Rv.Day.0.vs.low.Oxygen.Day.4.rep.3 4101:::H37Rv.Day.0.vs.low.Oxygen.Day.4.rep.4 4101:::H37Rv.Day.0.vs.low.Oxygen.Day.4.rep.6 4101:::NRP.Day20..1 4101:::NRP.Day6..2 4107:::DIPED.10ug.mL.vs.DMSO.12h.1 4107:::DIPED.50ug.mL.vs.DMSO.12h.1 4107:::DIPED.5ug.mL.vs.DMSO.12h.2 4107:::Mtm.0.2ug.mL.vs.ctrl.12h.1 4107:::Mtm.0.2ug.mL.vs.ctrl.8h.1 4107:::Mtm.0.2ug.mL.vs.ctrl.8h.2 4107:::pH4.8vspH6.8..5.5h. 4107:::Rif.0.5ug.mL.vsDMSO.2.5h 4107:::UV.40J.vs.8h.2 4107:::UV.40J.vs.ctrl.12h.1 4107:::UV.40J.vs.ctrl.8h.1 4107:::X.109..0.1ug.mL..vs.DMSO..12h..GEO.acc.GSM28050. 4107:::X.109..1ug.mL..vs.DMSO..12h..replicate.1..GEO.ac.GSM28051. 4107:::X.109..1ug.mL..vs.DMSO..12h..replicate.2..GEO.acc.GSM28052. 4107:::X.241..0.1ug.mL..DMSO..12h..1..GEO.acc.GSM28046. 4107:::X0.1mMGSNO.20ug.mLCPZvsDMSO.6h 4107:::X0.1mMGSNO.20ug.mLCPZvsDMSO.6hA 4107:::X0.1mMGSNO.5ug.mLKCNvsDMSO.6h 4107:::X0.2ug.mL.Mtmvsctrl..2h. 4107:::X0.2ug.mL.Mtmvsctrl..2h.A 4107:::X0.2ug.mL.Mtmvsctrl..2h.B 4107:::X0.2ug.mL.PA824.DMSO..6h..1 4107:::X0.4mM.NaN3.DMSO 4107:::X0.4ug.mL.PA824.DMSO..6h..1 4107:::X0.4ug.mL.PA824.DMSO..6h..2 4107:::X0.4ug.mL.PA824.DMSO..6h..3 4107:::X0.4ug.mL.PA824.DMSO..6h..4 4107:::X0.5ug.mL..111891vsDMSO.6h 4107:::X0.5ug.mL..121940vsDMSO.6h 4107:::X0.5ug.mL..124196vsDMSO..6h 4107:::X1.ug.mL..111891vsDMSO..6h 4107:::X100uM.Dipyridylvsctrl..6h 4107:::X100uM.DipyridylvsCtrl..6hA 4107:::X10ug.mL..109.DMSO..6h 4107:::X10ug.mL..59.DMSO..6h 4107:::X10ug.mL.ChlorprovsEtOH 4107:::X10ug.mL.ChlorprovsEtOH..6h 4107:::X10ug.mL.clofazimine.DMSO..6h 4107:::X10ug.mL.EconazolevsEtOH..6h 4107:::X10ug.mL.EMBvsDMSO..6hA 4107:::X10ug.mL.TriclosanvsDMSO..6h 4107:::X10ug.mL.TriclosanvsDMSO..6hA 4107:::X10ug.mL.TRZ.DMSO..6h..1 4107:::X10ug.mL.TRZ.DMSO..6h..2 4107:::X12.5ug.mL.AntimycinvsDMSO..6h 4107:::X13ug.mL.clfzine.DMSO..6h..1 4107:::X13ug.mL.clfzine.DMSO..6h..2 4107:::X150uM.Deferroxaminevsctrl..6hA 4107:::X1mM.DNP.DMSO..6h..1 4107:::X1ug.mL..124196vsDMSO..6hA 4107:::X20mJ.UVvsctrl..6h. 4107:::X20ug.mL.chlorprmz.DMSO..6h..1 4107:::X20ug.mL.chlorprmz.DMSO..6h..2 4107:::X20ug.mL.CPZvsDMSO..6h 4107:::X20ug.mL.CPZvsDMSO..6h.A 4107:::X20ug.mL.Prcp.6776.DMSO..6h..1 4107:::X20ug.mLProcept6778vsDMSO.6h 4107:::X20ug.mLProcept6778vsDMSO.6hA 4107:::X20ug.mLProcept6778vsDMSO.6hB 4107:::X24ug.mL.cltrmazole.DMS..6h..3 4107:::X24ug.mL.Econazole.DMSO..6h..1 4107:::X24ug.mL.Econazole.DMSO..6h..2 4107:::X250uM.DeferroxaminevsDMSO..6h 4107:::X25ug.mL.AntimycinvsDMSO..6h 4107:::X25ug.mL.CPZvsDMSO..6h.A 4107:::X25ug.mL.CPZvsDMSO..6h.B 4107:::X25ug.mLCPZ.0.1mMGSNO.DMSO..1 4107:::X25ug.mLCPZ.0.1mMGSNO.DMSO..2 4107:::X25ug.mLCPZ.0.1mMGSNO.DMSO..3 4107:::X25ug.mLCPZ.0.1mMGSNOvsDMSO.A 4107:::X2mM.DTTvsDMSO..6h 4107:::X2ug.mL.PA824.DMSO..6h..1 4107:::X2ug.mL.PA824.DMSO..6h..2 4107:::X30ug.mLProcept6776vsDMSO.6h 4107:::X40mJ.UV.ctrl..6h. 4107:::X40ug.mL.5CL.pH5.6..2h..2 4107:::X4mM.H2O2.ctrl..4h...1 4107:::X4mM.H2O2vsctrl..2h. 4107:::X50ug.mL.Triclosan.EtOH 4107:::X50ug.mLAntimycinAvsDMSO..6hA 4107:::X50uM.CCCP.DMSO..6h..1 4107:::X50uM.CCCP.DMSO..6h..2 4107:::X50uM.CCCPvsDMSO..6h 4107:::X50uM.NigericinvsDMSO..6h.A 4107:::X5ug.mL.CFZ.0.1mM.GSNO.DMSO..1 4107:::X5ug.mL.KCN.DMSO..6h..2 4107:::X5ug.mLProcept.6778vsDMSO.6h 4107:::X5ug.mLProcept.6778vsDMSO.6hA 4107:::X60J.UV.ctrl..2h. 4107:::X60ug.mL.ChlorprovsEtOH..6h 4363:::H37Rv.hypoxia.1.day.rep.2 4365:::H37Rv.diamide.1h.rep.3 4396:::H37Rv.cDNA.Cy3.vs.H37Rv.gDNA.Cy5..DS..rep.1 4396:::H37Rv.cDNA.Cy5.vs.H37Rv.gDNA.Cy3.rep.3 4396:::Strain.32.cDNA.Cy5.vs.H37Rv.gDNA.Cy3.rep.1 4396:::Strain.32.cDNA.Cy5.vs.H37Rv.gDNA.Cy3.rep.2 4396:::Strain.49.cDNA.Cy3.vs.H37Rv.gDNA.Cy5..DS..rep.3 4396:::Strain.49.cDNA.Cy5.vs.H37Rv.gDNA.Cy3.rep.3 4489:::MTB1254.Opp.KO.complemented.vs.Opp.KO.in.7H9OADC..OD..1.0.1 4489:::MTB1254.WT.vs.Rv3662c.3665c.KO.in.7H9OADC.Exp2..OD1.2 4575:::Extracted.Lung.Surfactant.30min.rep.2 4575:::Purified.Human.SP.A.Coated.2hrs.rep2 4575:::Purified.Human.SP.A.Uncoated.2hrs.rep3 4575:::Whole.Lung.Surfactant.2hrs.rep.1 4575:::Whole.Lung.Surfactant.30min.rep.2 4575:::Whole.Lung.Surfactant.30min.rep.4 4583:::X0.2ug.ml.PA.824.vs.DMSO.6hrs.rep.1 4583:::X0.2ug.ml.PA.824.vs.DMSO.6hrs.rep.2 4583:::X0.32ug.mL.Cerulenin.vs.Ethanol.6hrs.rep.2 4583:::X0.4ug.ml.PA.824.vs.DMSO.6hrs.rep.1 4583:::X0.4ug.ml.PA.824.vs.DMSO.6hrs.rep.3 4583:::X0.4ug.ml.PA.824.vs.DMSO.6hrs.rep.4 4583:::X0.5ug.mL.Cerulenin.vs.DMSO..6hrs.rep.2 4583:::X0.5ug.mL.Cerulenin.vs.Ethanol..6hrs.rep.1 4583:::X130ug.ml.TLM.vs.DMSO.6hrs.rep.2 4583:::X2ug.ml.PA.824.vs.DMSO.6hrs.rep.2 4583:::X5ug.ml.KCN.vs.DMSO.6hrs.rep.1 4583:::X5ug.ml.KCN.vs.DMSO.6hrs.rep.2 4599:::H37Rv.vs.SigE.mutant.24hrs.after.macrophage.infection.rep.2 4615:::AA_30uM_10m_01 4615:::AA_30uM_30min_02 4615:::AA_60uM_24h_02 4615:::Acetate.3mM.60m.04 4615:::CK_OA_NA_0.05_2h 4615:::L2A_30uM_10min_03 4615:::L2A_30uM_10min_08 4615:::L2A_30uM_1h_01 4615:::MTB1254.B4.1.Compl._OA_30MIN_02 4615:::MTB1254.B4.1.Compl._OA_30MIN_04 4615:::MTB1370_PA50_1h_04 4615:::OA_50uM_10min_06 4615:::OA_50uM_1h_01 4615:::OA_50uM_1h_02 4615:::OA_50uM_1h_07 4615:::PA_5.uM_10min_02 4615:::PA_50uM_24h.PA_50uM_1h_01 4615:::Rv_TA_OA30_30mim_03 4615:::Rv.MT71_100503_01 4615:::Rv.MT90_100503_01 4615:::Test_361.1 4615:::X7H9Cy3.MDGCy5.01 4615:::X7H9Cy3.MDGCy5.03 4630:::H37Rv.wild.type.Cy3.vs.Rv0485.Tn.mutant.Cy5.rep.3 4696:::H37Rv.wt.vs.dosS.dosT.null.anaerobic.Gaspak.4hr.rep.2 4696:::H37Rv.wt.vs.dosS.null.anaerobic.Gaspak.24hr.rep.1 4696:::H37Rv.wt.vs.dosS.null.nitric.oxide.treatment.1hr.rep.3 4696:::H37Rv.wt.vs.dosS.null.nitric.oxide.treatment.1hr.rep.4 4696:::H37Rv.wt.vs.dosT.null.rapid.anaerobic.dormancy.day.6.rep.2 4699:::CDC1551.Ctrl.vs.clinical.isolate.1797.03_EAI.rep.1 4699:::CDC1551.Ctrl.vs.clinical.isolate.1934.03_Beijing.rep.1 4699:::CDC1551.Ctrl.vs.clinical.isolate.2169.99_Uganda.rep.2 4703:::Clinical.isolate.10517.01_Afri2.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.1934.03_Beijing.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.2169.99_Uganda.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.2169.99_Uganda.extra.vs.intracellular.in.resting.macrophages.rep.2 4703:::Clinical.isolate.2333.99_Uganda.extra.vs.intracellular.in.resting.macrophages.rep.1 4703:::Clinical.isolate.4850.03_EAI.extra.vs.intracellular.in.resting.macrophages.rep.2 4704:::Clinical.isolate.12954.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::Clinical.isolate.2333.99_Uganda.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::Clinical.isolate.4130.02_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::Clinical.isolate.4850.03_EAI.extra.vs.intracellular.in.activated.macrophages.rep.1 4704:::Clinical.isolate.947.01_EAI.extra.vs.intracellular.in.activated.macrophages.rep.1 4731:::X0.4ug.ml.PA.824.vs.DMSO.6hrs.rep.2 4731:::X2ug.ml.PA.824.vs.DMSO.6hrs.rep.1 4735:::BCG.wild.type.vs.BCG.with.empty.pMV361.at.OD.0.4.rep.1 4735:::BCG.wild.type.vs.BCG.with.empty.pMV361.at.OD.0.4.rep.2 4735:::BCG.wild.type.vs.BCG.with.empty.pMV361.at.OD.0.4.rep.3 4735:::BCG.wild.type.vs.BCG.with.empty.pMV361.at.OD.0.4.rep.4 4735:::BCG.wild.type.vs.BCG.with.empty.pMV361.at.OD.0.4.rep.5 4735:::BCG.wild.type.vs.BCG.with.pMFdosR.at.OD.0.2.rep.3 4735:::BCG.wild.type.vs.BCG.with.pMFdosR.at.OD.0.2.rep.5 4795:::CDC1551.ctrl.vs.40.ug.ml.Thioridazine.2hr.rep.2 4802:::H37Rv.ctrl.vs.relE1.overexpression.24.hr.rep.2 4802:::H37Rv.ctrl.vs.relE3.overexpression.24.hr.rep.1 4815:::H37Rv.reaeration.for.4hrs.rep.4 4815:::H37Rv.reaeration.for.6hrs.rep.3 Raghavan_Nature2008:::espR.mutant..R...rep2 Raghavan_Nature2008:::espR.mutant.complemented.with.N.terminal.Flag.espR..RFL..rep1 Raghavan_Nature2008:::espR.mutant.complemented.with.WT.espR..R...rep2 RV0870C NA 0.0809388911371914 0.161877782274383 -0.78240928099285 -1.02522595440442 0.782409280992851 0.643832088591295 -0.0306586708852998 0.919760126558994 -0.245269367082398 0 0 0.149886835439243 0.524603924037352 1.64875518983168 2.21083082272884 2.51060449360733 2.47313278474752 1.57381177211206 0 2.02347227842979 1.94852886071016 0.936792721495271 1.68622689869149 0.262301962018676 1.16162297465414 1.34898151895319 1.94852886071016 1.386453227813 0.524603924037352 1.61128348097187 1.19909468351395 1.23656639237376 1.53634006325224 0.487132215177541 -0.412188797457919 -0.262301962018676 -0.487132215177541 -0.824377594915839 -0.224830253158865 -0.824377594915839 1.386453227813 0.524603924037352 -1.01173613921489 -0.562075632897163 -0.374717088598108 -0.936792721495271 0.044966050631773 -0.429221392394197 -0.459880063279497 NA -0.521197405050096 -0.0306586708852997 -0.551856075935396 0.705149430361895 0.827784113903094 0.153293354426499 1.83952025311799 -0.289067468347112 0.80296518985309 0.546016329100101 -0.794935537954559 -0.698579715172188 0.0240889556955927 -1.03582509491049 0.698579715172188 -0.554045980998632 -1.02639898181221 0.058651370389269 -0.733142129865864 -0.205279796362442 -0.205279796362442 0.351908222335615 1.87684385245661 -0.498536648308788 -0.32258253714098 0.410559592724884 -0.439885277919519 -0.762467815060499 -1.14370172259075 -1.58358700051027 -0.762467815060499 1.73021542648344 1.7008897412888 1.37830720414782 0.821119185449768 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POSITION A C G T 1 0 0.8 0 0.2 2 0.5 0 0.2 0.3 3 0 0 1 0 4 0 0.5 0 0.5 5 0.3 0.1 0.6 0 6 0.1 0.6 0.1 0.2 7 0.7 0.2 0 0.1 8 0.2 0.7 0 0.1 9 0 0.1 0.6 0.3 10 0 0.7 0 0.3 11 0.2 0.8 0 0 12 0.2 0 0.5 0.3 13 0.3 0.2 0.5 0 14 0 0.9 0 0.1 15 0 0.3 0 0.7 16 0.1 0 0.4 0.5 17 0.2 0.4 0.4 0 18 0.1 0 0.6 0.3 19 0.8 0 0 0.2 20 0.2 0 0.8 0 21 0.6 0 0.4 0

POSITION A C G T 1 0 0 0 1 2 0 0.25 0.75 0 3 0 1 0 0 4 0 1 0 0 5 0 0.5 0 0.5 6 0 0 0 1 7 0 0 0 1 8 0 0 1 0 9 0.25 0 0.75 0 10 0 0.75 0 0.25 11 0.75 0 0.25 0 12 0 0 0.75 0.25 13 0 0 1 0 14 0.75 0.25 0 0 15 1 0 0 0