Expression clusters for osmotic stress responsive genes

List of all 175 genes with changes greater than 2 fold under salt treatment with their respective cluster assignments (0 – 5). Probe-set refers to the Affymetrix designation. Score refers to the supercoiling-dependent score as described in Figure 3. Clusters correspond to those depicted in Figure 2.

Probe Set	product	gene	cluster	score
aceA_b4015_st	isocitrate lyase	aceA	0	7
aceB_b4014_st	malate synthase A	aceB	0	7
acnA_b1276_st	aconitate hydrase 1	acnA	0	8
b0753_st	putative homeobox protein	#N/A	0	7
b1481_st	orf, hypothetical protein	#N/A	0	7
b1664_st	possible enzyme	#N/A	0	9
b1724_st	orf, hypothetical protein	#N/A	0	8
b1836_st	orf, hypothetical protein	#N/A	0	7
b1957_st	orf, hypothetical protein	#N/A	0	7
b2097_st	orf, hypothetical protein	#N/A	0	6
b2809_st	orf, hypothetical protein	#N/A	0	10
b3100_st	orf, hypothetical protein	#N/A	0	5
bax_b3570_f_st	putative ATP-binding protein	bax	0	8
betA_b0311_st	choline dehydrogenase, a flavoprotein	betA	0	6
betB_b0312_st	NAD+-dependent betaine aldehyde dehydrogenase	betB	0	6
betI_b0313_st	probably transcriptional repressor of bet genes	betI	0	6
betT_b0314_st	high-affinity choline transport	betT	0	7
btuE_b1710_st	vitamin B12 transport	btuE	0	8
dps_b0812_st	global regulator, starvation conditions	dps	0	9
elaB_b2266_st	orf, hypothetical protein	elaB	0	6
gcd_b0124_st	glucose dehydrogenase	gcd	0	8
grxB_b1064_st	glutaredoxin 2	grxB	0	8
himA_b1712_st	integration host factor (IHF), alpha subunit; site specific recombination	ihfA	0	7
katE_b1732_st	catalase; hydroperoxidase HPII(III)	katE	0	6
miaA_b4171_st	delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase	miaA	0	7
nlpD_b2742_st	lipoprotein	nlpD	0	8
osmC_b1482_st	osmotically inducible protein	osmC	0	6
osmE_b1739_st	activator of ntrL gene	osmE	0	8
osmY_b4376_st	hyperosmotically inducible periplasmic protein	osmY	0	7
otsA_b1896_st	trehalose-6-phosphate synthase	otsA	0	8
otsB_b1897_st	trehalose-6-phosphate phophatase, biosynthetic	otsB	0	8
poxB_b0871_st	pyruvate oxidase	poxB	0	8
proV_b2677_st	ATP-binding component of transport system for glycine, betaine and proline	proV	0	9
proW_b2678_st	high-affinity transport system for glycine betaine and proline	proW	0	8
proX_b2679_st	high-affinity transport system for glycine betaine and proline	proX	0	9
rpoS_b2741_st	RNA polymerase, sigma S (sigma38) factor; synthesis of many growth phase related proteins	rpoS	0	9
rpsV_b1480_st	30S ribosomal subunit protein S22	rpsV	0	7
sugE_b4148_st	suppresses groEL, may be chaperone	sugE	0	8
talA_b2464_st	transaldolase A	talA	0	5
tktB_b2465_st	transketolase 2 isozyme	tktB	0	8
treF_b3519_st	cytoplasmic trehalase	treF	0	5
wrbA_b1004_st	trp repressor binding protein; affects association of trp repressor and operator	wrbA	0	8
yacK_b0123_st	orf, hypothetical protein	yacK	0	9
ybaL_b0478_st	putative transport protein	ybaL	0	8
ybaY_b0453_st	glycoprotein/polysaccharide metabolism	ybaY	0	10
ybeL_b0643_st	putative alpha helical protein	ybeL	0	8
yccJ_b1003_st	orf, hypothetical protein	yccJ	0	5
yeaQ_b1795_st	orf, hypothetical protein	yeaQ	0	5
ygaM_b2672_st	orf, hypothetical protein	ygaM	0	9
ygaU_b2665_st	orf, hypothetical protein	ygaU	0	7
yggB_b2924_st	putative transport protein	yggB	0	9
ygjG_b3073_st	probable ornithine aminotransferase	ygjG	0	5
yhiX_b3516_st	putative ARAC-type regulatory protein	yhiX	0	7
yjbJ_b4045_st	orf, hypothetical protein	yjbJ	0	6
ykfE_b0220_st	orf, hypothetical protein	ykfE	0	8
ynhG_b1678_st	orf, hypothetical protein	ynhG	0	8
yqjC_b3097_st	orf, hypothetical protein	yqjC	0	6
yqjD_b3098_st	orf, hypothetical protein	yqjD	0	6
yqjE_b3099_st	orf, hypothetical protein	yqjE	0	5
yrbL_b3207_st	orf, hypothetical protein	yrbL	0	10
ytfK_b4217_st	orf, hypothetical protein	ytfK	0	7
oppC_b1245_st	homolog of Salmonella oligopeptide transport permease protein	oppC	1	6
oppD_b1246_st	homolog of Salmonella ATP-binding protein of oligopeptide ABC transport system	oppD	1	6
oppF_b1247_st	homolog of Salmonella ATP-binding protein of oligopeptide ABC transport system	oppF	1	6
trkH_b3849_st	potassium uptake, requires TrkE	trkH	1	6
yijE_b3943_st	orf, hypothetical protein	yijE	1	6
yrbG_b3196_st	orf, hypothetical protein	yrbG	1	5
aldA_b1415_st	aldehyde dehydrogenase, NAD-linked	aldA	2	5
apt_b0469_st	adenine phosphoribosyltransferase	apt	2	8
argS_b1876_st	arginine tRNA synthetase	argS	2	9
b0725_st	orf, hypothetical protein	#N/A	2	7
b1722_st	orf, hypothetical protein	#N/A	2	9
corA_b3816_st	Mg2+ transport, system I	corA	2	6
dctA_b3528_st	uptake of C4-dicarboxylic acids	dctA	2	5
fabB_b2323_st	3-oxoacyl-[acyl-carrier-protein] synthase I	fabB	2	7
flgB_b1073_st	flagellar biosynthesis, cell-proximal portion of basal-body rod	flgB	2	7
flgC_b1074_st	flagellar biosynthesis, cell-proximal portion of basal-body rod	flgC	2	8
flgE_b1076_st	flagellar biosynthesis, hook protein	flgE	2	9
fliJ_b1942_st	flagellar fliJ protein	fliJ	2	6
gatA_b2094_st	galactitol-specific enzyme IIA of phosphotransferase system	gatA	2	5
gatB_b2093_st	galactitol-specific enzyme IIB of phosphotransferase system	gatB	2	6
gatC_b2092_st	PTS system galactitol-specific enzyme IIC	gatC	2	7
gatD_b2091_st	galactitol-1-phosphate dehydrogenase	gatD	2	6
gatR_2_b2090_f_st	split galactitol utilization operon repressor, fragment 2	gatR	2	6
gatY_b2096_st	tagatose-bisphosphate aldolase 1	gatY	2	5
gatZ_b2095_st	putative tagatose 6-phosphate kinase 1	gatZ	2	5
gcvP_b2903_st	glycine decarboxylase, P protein of glycine cleavage system	gcvP	2	5
lldD_b3605_st	L-lactate dehydrogenase	lldD	2	5
mrdA_b0635_st	cell elongation, e phase; peptidoglycan synthetase; penicillin-binding protein 2	mrdA	2	6
ompF_b0929_st	outer membrane protein 1a (Ia;b;F)	ompF	2	7
pal_b0741_st	peptidoglycan-associated lipoprotein	pal	2	6
proA_b0243_st	gamma-glutamylphosphate reductase	proA	2	7
sdhA_b0723_st	succinate dehydrogenase, flavoprotein subunit	sdhA	2	6
sdhC_b0721_st	succinate dehydrogenase, cytochrome b556	sdhC	2	6
suhB_b2533_st	enhances synthesis of sigma32 in mutant; extragenic suppressor, may modulate RNAse III lethal action	suhB	2	7
treC_b4239_st	trehalase 6-P hydrolase	treC	2	6
upp_b2498_st	uracil phosphoribosyltransferase	upp	2	7
yaaF_b0030_st	orf, hypothetical protein	yaaF	2	8
ychF_b1203_st	putative GTP-binding protein	ychF	2	10
ydbP_b1390_st	orf, hypothetical protein	paaC	2	7
yedF_b1930_st	orf, hypothetical protein	yedF	2	7
yeeF_b2014_st	putative amino acid/amine transport protein	yeeF	2	9
yehZ_b2131_st	putative transport system permease protein	yehZ	2	6
yfeD_b2399_st	orf, hypothetical protein	yfeD	2	10
yifE_b3764_st	orf, hypothetical protein	yifE	2	6
yqgB_b2939_st	orf, hypothetical protein	yqgB	2	9
b2084_st	orf, hypothetical protein	#N/A	3	5
b2085_st	orf, hypothetical protein	#N/A	3	7
b2373_st	putative enzyme	#N/A	3	5
b2374_st	putative enzyme	#N/A	3	7
b2666_st	orf, hypothetical protein	#N/A	3	7
b2680_st	orf, hypothetical protein	#N/A	3	5
ffs_b0455_st	unknown-type	ffs	3	6
gapC_1_b1417_st	glyceraldehyde 3-phosphate dehydrogenase C, interrupted	gapC	3	8
gapC_2_b1416_st	glyceraldehyde-3-phosphate dehydrogenase (second fragment)	gapC	3	7
hdhA_b1619_st	NAD-dependent 7alpha-hydroxysteroid dehydrogenase, dehydroxylation of bile acids	hdhA	3	8
ogrK_b2082_st	prophage P2 ogr protein	ogrK	3	5
ompX_b0814_st	outer membrane protein X	ompX	3	6
oppA_b1243_st	oligopeptide transport; periplasmic binding protein	oppA	3	6
osmB_b1283_st	osmotically inducible lipoprotein	osmB	3	6
proP_b4111_st	low-affinity transport system; proline permease II	proP	3	5
ycdF_b1005_st	orf, hypothetical protein	#N/A	3	8
ydgA_b1614_st	orf, hypothetical protein	ydgA	3	6
yfhB_b2560_st	orf, hypothetical protein	yfhB	3	8
asnA_b3744_st	asparagine synthetase A	asnA	4	8
asnB_b0674_st	asparagine synthetase B	asnB	4	5
b0005_st	orf, hypothetical protein	#N/A	4	7
b1452_st	putative receptor	#N/A	4	6
b1973_st	orf, hypothetical protein	#N/A	4	7
b4256_st	orf, hypothetical protein	#N/A	4	6
dinI_b1061_st	damage-inducible protein I	dinI	4	7
dsbB_b1185_st	reoxidizes DsbA protein following formation of disulfide bond in P-ring of flagella.	dsbB	4	6
folE_b2153_st	GTP cyclohydrolase I	folE	4	6
ilvC_b3774_st	ketol-acid reductoisomerase	ilvC	4	5
ilvG_1_b3767_st	acetolactate synthase II, large subunit, cryptic, interrupted	ilvG	4	7
ilvN_b3670_st	acetolactate synthase I, valine sensitive, small subunit	ilvN	4	5
metE_b3829_st	tetrahydropteroyltriglutamate methyltransferase	metE	4	6
purF_b2312_st	amidophosphoribosyltransferase = PRPP amidotransferase	purF	4	8
pyrC_b1062_st	dihydro-orotase	pyrC	4	6
pyrD_b0945_st	dihydro-orotate dehydrogenase	pyrD	4	6
tdcB_b3117_st	threonine dehydratase, catabolic	tdcB	4	7
thrA_b0002_st	aspartokinase I, homoserine dehydrogenase I	thrA	4	6
thrB_b0003_st	homoserine kinase	thrB	4	6
thrC_b0004_st	threonine synthase	thrC	4	6
ybaN_b0468_st	putative gene 58	ybaN	4	6
ybjE_b0874_st	putative surface protein	ybjE	4	5
ycdO_b1018_st	orf, hypothetical protein	ycdO	4	6
yhcL_b3227_st	putative transport protein	yhcL	4	7
yhjE_b3523_st	putative transport protein	yhjE	4	9
yieG_b3714_st	putative membrane / transport protein	yieG	4	5
ykgM_b0296_st	putative ribosomal protein	ykgM	4	5
b1446_st	orf, hypothetical protein	#N/A	5	7
deoB_b4383_st	phosphopentomutase	deoB	5	6
folA_b0048_st	dihydrofolate reductase type I; trimethoprim resistance	folA	5	6
ivbL_b3672_st	ilvB operon leader peptide	ivbL	5	6
lamB_b4036_st	phage lambda receptor protein; maltose high-affinity receptor	lamB	5	5
malE_b4034_st	periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis	malE	5	5
malK_b4035_st	ATP-binding component of transport system for maltose	malK	5	7
manX_b1817_st	PTS enzyme IIAB, mannose-specific	manX	5	6
manY_b1818_st	PTS enzyme IIC, mannose-specific	manY	5	6
manZ_b1819_st	PTS enzyme IID, mannose-specific	manZ	5	5
ndk_b2518_st	nucleoside diphosphate kinase	ndk	5	7
nmpC_b0553_st	outer membrane porin protein; locus of qsr prophage	nmpC	5	6
nupC_b2393_st	permease of transport system for 3 nucleosides	nupC	5	5
pheP_b0576_st	phenylalanine-specific transport system	pheP	5	7
ptsG_b1101_st	PTS system, glucose-specific IIBC component	ptsG	5	5
rbsD_b3748_st	D-ribose high-affinity transport system; membrane-associated protein	rbsD	5	7
spf_b3864_st	unknown-type	spf	5	6
thrL_b0001_st	thr operon leader peptide	thrL	5	5
tolR_b0738_st	putative inner membrane protein, involved in the tonB-independent uptake of group A colicins	tolR	5	5
ybcU_b0557_st	bacteriophage lambda Bor protein homolog	borD	5	6
yebH_b1822_st	putative enzyme	rrmA	5	6
yjcQ_b4081_st	putative enzyme	yjcQ	5	6
yjcV_b4086_st	putative transport system permease protein	alsC	5	7
yqeF_b2844_st	putative acyltransferase	yqeF	5	8