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