TABLE 3.

Functional classification of genes with statistically significant decreases and increases in mRNA level in E. coli BW25113 ΔptsA and WT strains^a

Category and expression status	GO concerned	P value	Genes involved
Overexpressed
Secondary metabolism	GO:0019563; glycerol catabolic process	3.82E−11	gldA, hybA, glpK, glpC, glpB, glpD, glpA
	GO:0045333; cellular respiration	2.90E−19	frdB, dmsA, dmsB, dmsC, hybB, fdnG, fdnH, frdA, frdC, frdD, hyaB, hybO, napB, napC, narG, narH, nirB, nirD, napA, glpD, glpA, glpB, glpC, ndh, hybA, hybC, hyaC, yjjI, cydA, cydB
	GO:0071941; nitrogen cycle metabolic process	1.75E−09	argF, napC, glnL, glnG, nirB, narG, nirD, nirC, narJ, narK, narH, napA, nrfA
	GO:0019394; glucarate catabolic process	7.97E−06	garL, gudD, garR, garK
Response to stimuli	GO:0046688; response to copper ion	1.14E−08	cusS, copA, cusA, cusB, cusC, cusF, cusR, yobA, cueO
	GO:0009432; SOS response	1.74E−07	recA, recN, sulA, umuC, umuD, yebG, recX, dinI, lexA, dinD, dinG
Transport	GO:0015886; heme transport	2.41E−08	ccmA, ccmD, ccmB, ccmC, ccmF, dppF, ccmE, dppC
	GO:0015675; nickel cation transport	2.05E−05	nikB, nikC, nikE, nikD, nikA
	GO:0006857; oligopeptide transport	8.02E−04	dppC, dppF, oppB, oppC, oppF, oppD, oppA
Underexpressed
Iron	GO:0055072; iron ion homeostasis	7.40E−15	fepA, efeB, cirA, yqjH, fhuF, bfr, iscU, fhuA, fhuB, fhuC, fhuD, feoA, fepB, fes, fhuE, fecI, fecR, fepD, fepG, fepC, fiu
	GO:0016226; iron-sulfur cluster assembly	2.05E−06	iscS, iscU, erpA, sufB, sufD, sufA, sufC, sufE, sufS
Secondary metabolism	GO:0009447; putrescine catabolic process	3.95E−10	patA, patD, puuE, puuA, puuD, puuP, puuR, puuC, puuB
	GO:0009065; glutamine family amino acid catabolic process	1.41E−05	putA, astE, astD, astC, astB, astA, gabD, aldA
	GO:0006790; sulfur compound metabolic process	7.66E−08	prpB, prpD, prpE, prpR, fadH, fadI, fadE, fadM, fadD, fadA, fadB, yqeF
Tricarboxylic acid	GO:0006099; tricarboxylic acid cycle	4.17E−09	sdhC, sdhB, acnA, gltA, fumA, fumC, sdhA, aceB, aceA, aceK, sucA, prpC, prpD
Fatty acids	GO:0009062; fatty acid catabolic process	4.62E−09	prpB, prpD, prpE, prpR, fadH, fadI, fadE, fadM, fadD, fadA, fadB, yqeF
	GO:0009712; catechol-containing compound metabolic process	8.28E−08	entA, entC, entE, entH, entF, entB, fes, paaJ
Hydrogen sulfide	GO:0070814; hydrogen sulfide biosynthetic process	1.25E−07	astE, astD, astC, astB, astA, gabD
Enterobactin	GO:0042930; enterobactin transport	3.10E−06	fepA, fepD, fepG, fepC, fepB, entS

^aLevels in E. coli BW25113 ΔptsA strain in M9-DHA medium were compared to those for E. coli BW25113 WT strain in M9-DHA medium. The Clusters of Orthologous Groups (COG) were used for grouping.