TABLE S6Hypergeometric probability analysis of genes determined to be >2.5-fold downregulated in sputum compared to in vitro H37Rvgrowth by amplified microarray
Subset of genes enriched / No. genes / Hypergeometricp value1
2.5 fold repressed NRP2 v Aerobic ANOVA p0.05 B+H This study / 56 / 3.80E-36
Intracellular_Murine Macrophage Repressed Schnappinger et al., 2003 [3] / 64 / 8.16E-35
Slow Growth Repressed >1.2 fold_BCG Beste et al., 2007 [9] / 50 / 8.75E-20
Nutrient Starvation Repressed 4 or 24 or 96 h Betts et al., 2002 [10] / 81 / 4.61E-14
Murine hollow fibre model Repressed v log phase H37Rv Karakousis et al., 2004 [12] / 21 / 1.40E-11
sigE repressed genes in sigE KO v WT H37Rv Manganelli et al., 2001 [13] / 18 / 3.57E-11
II.A.1 Ribosomal protein synthesis and modification [2] / 21 / 3.96E-10
I.B.6.a Aerobic [2] / 14 / 7.47E-09
PhoP regulon genes induced in WT v mutant Walters et al., 2006 [17] / 16 / 4.84E-08
sigD regulon Calamita et al., 2005 [11] / 18 / 2.08E-07
2.5 fold repressed NRP1 v Aerobic ANOVA p0.05 B+H This study / 7 / 4.24E-07
Stationary Phase Low Glu Induced genes Hampshire et al., 2004 [18] / 40 / 5.57E-07
I.B.6 Respiration [2] / 17 / 1.13E-06
I.B.8 ATP-proton motive force [2] / 6 / 4.44E-06
sigD Repressed knockout v WT H37Rv Raman et al., 2004 [22] / 14 / 5.33E-06
Genes required for mycobacterial growth in vitro Sassetti et al., 2003 [14] / 75 / 7.25E-06
II.A Synthesis and modification of macromolecules [2] / 34 / 2.20E-05
I.B Energy metabolism [2] / 42 / 2.53E-05
Nutrient Starvation Induced 4 or 24 or 96 h Betts et al., 2002 [10] / 55 / 8.30E-05
1 Small molecule metabolism [2] / 102 / 0.00342
II.A.6 Protein translation and modification [2] / 5 / 0.00385
I.F Purines, pyrimidines, nucleosides and nucleotides [2] / 11 / 0.0047
Genes Required for Survival in Macrophages. Rengarajan et al., 2005 [23] / 18 / 0.00611
I.B.1 Glycolysis [2] / 4 / 0.00982
I.H.2 Modification of fatty and mycolic acids [2] / 4 / 0.0176
IV.A Virulence [2] / 7 / 0.0219
BALBc vs 7H9 broth at 45 days Repressed Talaat et al., 2007 [15] / 18 / 0.0228
I.H Lipid biosynthesis [2] / 10 / 0.0229
I.H.1 Synthesis of fatty and mycolic acids [2] / 5 / 0.0424
dosR-dependent genes repressed in vitro Kendall et al., 2004 [5] / 4 / 0.0505
I.F.1 Purine ribonucleotide biosynthesis [2] / 4 / 0.0595
1A cut-off of p<0.05 was applied.
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