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Table 1 Ranalexin response modules

From: Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus

Module description

Ranalexin Altered Gene Set

Additional Genes In Module

False discovery rate adjusted p-value

+ Val/Leu/Ile metabolism

SAR2141, SAR2143, SAR2144, SAR2146, SAR2147, SAR2148 (6/7* genes)

SAR2297

<9.0E-5*

+ Na+/H+ antiporters (mnh operons)

SAR0629-SAR0635, SAR0908 (8/17* genes)

SAR0909-SAR0915, SAR0627, SAR0628

<9.0E-5*

+ Persister formation, phosphate transport (pstSCAB-phoU operon)

SAR1400-SAR1402, SAR1398 (4/4 genes)

-

1.2E-4

+ Chaperones, stress response

SAR0938, SAR1657, SAR1658 (3/3 genes)

-

0.027

+ Osmoprotectant transport

SAR2536-SAR2538 (3/6 genes)

3 genes: SAR2535, SAR0775, SAR0776

0.046

- Virulence factors (ESAT-6 system)

SAR0279, SAR0281-0284, SAR0287, SAR0288 (7/12* genes)

SAR0285, SAR0286, SAR0289, SAR0290, SAR0291

<1.9E-4*

- High-affinity metal ion transport (Fe)

SAR0787-SAR0790 (4/5 genes)

SAR1011

0.0019

- Virulence factors (Colonization, immuno-modulation)

SAR0567, SAR0847, SAR2508 SAR2709 (4/16 genes)

SA0566, SAR0842, SAR1102, SAR1103, SAR1223, SAR1489, SAR1802, SAR1841, SAR2383, SAR2421, SAR2580, SAR2734

0.0062

- High-affinity metal ion transport (Fe, Zn, Mn, Mo)

SAR0274, SAR0643, SAR2594, SAR2452 (4/9 genes)

SAR1633, SAR1928, SAR2361, SAR2543, SAR2544

0.0062

- Virulence (inferred from network)

SAR0292-SAR0294 (3/3 genes)

-

0.025

- Cell division

SAR1177-SAR1179 (3/4 genes)

SAR1175

0.028

  1. A prefix '+' in the first column indicates modules with upregulated genes, a prefix '-' downregulated genes. *No instances of these module coverage levels were observed in the appropriate random sampling. Therefore the background frequency was set to 1/100000 for estimation of p-values.