TABLE 2.

Gene categories in cold-stressed (5°C, 48 h) S. Typhimurium that were significantly (q < 0.05) regulated during infection of epithelial cells

Enriched gene categorya	No. of genes regulated	No. of genes in category	Regulation	FDR (q)b
Prophage functions	63	143	Induced	0
Plasmid functions	26	28	Induced	0
Transposon functions	27	44	Induced	0
SPV locus	4	4	Induced	0.04
Adaptations to atypical conditions	10	30	Induced	0.04
Cellular processes—DNA transformation	30	30	Induced	0
Energy metabolism—anaerobic	32	66	Induced	0.04
Synthesis and modification ribosomal proteins	37	61	Repressed	0
CogJ—translation	67	170	Repressed	0
Cellular processes—chemotaxis and motility	20	40	Repressed	0
Energy metabolism—pyruvate dehydrogenase	3	8	Repressed	0.02
Metabolism of surface polysaccharides and LPS	39	82	Repressed	0.04
Energy metabolism—aerobic	12	24	Repressed	0.04

^aSPV, Salmonella plasmid virulence locus.

^bFDR, false discovery rate.