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

BMC Genomics

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

		Genes regulated		FDR q-value		NES^H
Gene set	Size of gene set^A	Aerobic^B	H₂O₂^C	Aerobic^D	H₂O₂^E	Aerobic^F	H₂O₂^G
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

^ABased on the KEGG database for S. Typhimurium LT2.
^BNumber of genes predicted to contribute to the enrichment in aerobic growth in rich media.
^CNumber of genes predicted to contribute to the enrichment in response to H₂O₂.
^Dq-value for the pathway predicted to be regulated by ArcA in aerobic growth in rich media.
^Eq-value for the pathway predicted to be regulated by ArcA in response to H₂O₂.
^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.
^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.
^HNormalized enrichment score.

ISSN: 1471-2164