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Table 1 Pathways differentially regulated (q ≤ 0.25) by ArcA in response to H 2 O 2 and aerobiosis as determined by GSEA

From: Probing the ArcA regulon under aerobic/ROS conditions in Salmonella enterica serovar Typhimurium

   Genes regulated FDR q-value NESH
Gene set Size of gene setA AerobicB H2O2C AerobicD H2O2E AerobicF H2O2G
Glycerophospholipid metabolism 25 5 5 0.001 0.000 2.16 2.29
Purine metabolism 73 19 35 0.003 0.000 2.06 2.22
Pyrimidine metabolism 50 14 18 0.044 0.003 1.79 2.02
Lipopolisaccharide biosynthesis 26   17   0.004   1.98
Glutathione metabolism 16   8   0.005   1.94
Bacterial invasion of epithelial cells 8 8 5 0.002 0.012 −1.9 1.87
Glycolysis/gluconeogenesis 33 10 10 0.250 0.022 0.46 1.81
Biosynthesis of siderophore group non-ribosomal peptides 5   4   0.067   1.69
Glycerolipid metabolism 10 1 1 0.083 0.109 1.68 1.6
Flagellar assembly 34   7   0.189   1.5
Phosphotransferase system (PTS) 32 17 17 0.001 0.000 −1.88 −2.26
ABC transporters 124 46 29 0.005 0.022 −1.83 −1.86
Salmonella infection 16 8   0.001   −2.04  
Bacterial secretion system 28 12   0.005   −1.79  
Bacterial chemotaxis 22 6   0.049   −1.63  
Two-component system 88 11   0.096   −1.56  
Cyanoamino acid metabolism 6 3   0.129   −1.52  
Ascorbate and aldarate metabolism 8 3   0.117   −1.52  
Amino sugar and nucleotide sugar metabolism 50 14   0.213   −1.43  
Fructose and mannose metabolism 34 14   0.233   −1.43  
Starch and sucrose metabolism 26 14   0.244   −1.39  
Ribosome 45 28   0.004   2.01  
Riboflavin metabolism 8 3   0.113   1.63  
Cysteine and methionine metabolism 24 8   0.137   1.59  
  1. ABased on the KEGG database for S. Typhimurium LT2.
  2. BNumber of genes predicted to contribute to the enrichment in aerobic growth in rich media.
  3. CNumber of genes predicted to contribute to the enrichment in response to H2O2.
  4. Dq-value for the pathway predicted to be regulated by ArcA in aerobic growth in rich media.
  5. Eq-value for the pathway predicted to be regulated by ArcA in response to H2O2.
  6. FNormalized enrichment score for pathways under aerobic conditions. Positive values indicate pathways negatively regulated by ArcA, while negative values indicate pathways that are up-regulated by ArcA.
  7. GNormalized enrichment score for pathways under aerobic conditions after H2O2 exposure. Positive values indicate pathways positively regulated by ArcA, while negative ones indicate pathways that are downregulated by ArcA.
  8. HNormalized enrichment score.