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Table 3 Three major modules in gene co-expression networka

From: Snapshot of iron response in Shewanella oneidensis by gene network reconstruction

Gene

Annotation

Change in expression at:

  

C1'

C5'

C10'

C20'

C40'

C60'

F1'

F5'

F10'

F20'

F40'

F60'

Iron acquisition

             

SO0448

conserved hypothetical inner membrane protein

3.40

--

--

5.00

3.41

4.30

0.56

0.46

0.26

0.21

0.20

0.15

SO0449

conserved iron-regulated membrane protein

4.00

4.61

3.88

3.06

3.76

3.20

1.07

0.67

0.49

0.59

0.48

0.35

SO0744

iron(III) ABC transporter, periplasmic iron(III)-binding protein

2.92

3.42

3.72

3.61

5.40

6.93

0.50

0.16

0.12

0.12

0.20

0.17

SO1111

bacterioferritin subunit 2 (Bfr2)

0.53

0.45

0.41

0.36

0.41

0.56

2.56

3.41

6.00

--

5.75

5.61

SO1188

unknown inner membrane protein

8.66

9.94

10.62

14.47

10.91

8.38

0.47

0.12

0.09

0.11

0.24

0.10

SO1190

ABC-type Co2+ transporter, a periplasmic component

1.06

2.57

4.59

--

6.28

3.70

0.90

0.52

0.18

0.07

0.08

0.07

SO1482

TonB-dependent receptor

3.50

3.44

6.62

7.12

8.44

8.13

0.62

0.21

0.05

0.06

0.03

0.03

SO1755

phosphoglucomutase/phosphomannomutase family protein

1.37

1.63

2.09

2.77

3.31

4.19

0.55

0.38

0.27

0.21

0.26

0.21

SO1784

ferrous iron transport protein B (FeoB)

3.74

4.98

4.07

2.45

2.49

2.29

0.62

0.25

0.20

0.13

0.23

0.14

SO2039

signalling protein with EAL domain

3.09

3.89

3.39

4.86

4.81

--

--

--

--

--

--

--

SO2260

extragenic suppressor protein (SuhB)

0.59

0.49

0.43

 

0.41

0.45

2.52

1.78

2.49

6.21

3.63

5.58

SO2426

two component transcriptional regulator

11.65

13.67

10.06

7.88

8.90

10.00

0.57

0.11

0.07

0.06

0.05

0.06

SO2736

conserved hypothetical outer membrane protein

3.88

5.33

4.47

4.37

4.78

5.23

0.56

0.33

0.40

0.27

0.28

0.25

SO3025

unknown protein

1.85

2.54

3.71

5.24

6.75

6.11

0.71

0.28

0.25

0.23

0.23

0.16

SO3030

alcaligin biosynthesis enzyme (AlcA)

6.24

8.34

14.64

12.87

23.64

12.45

1.90

0.75

0.80

0.18

0.12

0.11

SO3032

alcaligin biosynthesis protein (AlcC)

1.65

1.80

3.94

9.20

21.09

19.42

1.23

--

0.72

0.14

0.42

--

SO3034

ferric iron reductase protein (AlcE)

1.07

1.02

1.60

3.76

5.51

5.25

0.65

1.01

0.50

0.15

0.18

0.11

SO3063

sodium:alanine symporter family protein

1.04

1.67

2.11

4.10

4.38

4.68

0.85

0.54

0.23

0.41

0.54

0.29

SO3065

colicin V production protein

--

--

0.33

0.35

0.37

0.42

2.16

--

1.29

2.73

2.93

3.30

SO3407

conserved iron-regulated membrane protein

11.36

17.13

18.98

18.04

13.31

10.14

0.68

0.10

0.05

0.06

0.13

0.04

SO3667

heme iron utilization protein

1.22

2.01

6.03

--

17.15

13.53

0.83

0.65

0.33

0.08

0.02

0.01

SO3668

HugX family protein

1.93

3.45

9.15

12.84

20.27

18.24

0.82

0.39

0.21

0.10

0.04

--

SO3669

heme transport protein (HugA)

19.42

41.21

56.72

--

74.82

69.78

0.44

0.07

0.03

0.04

0.04

--

SO3670

TonB1 protein

22.48

45.17

62.47

34.35

41.42

64.58

0.10

0.04

0.02

0.02

0.08

0.01

SO3671

TonB system transport protein (ExbB1)

16.33

37.79

50.11

56.59

51.37

56.36

0.59

0.05

0.02

0.03

0.03

--

SO3672

TonB system transport protein (ExbD1)

2.43

7.33

11.09

13.87

10.34

9.45

0.84

0.21

--

0.16

0.32

--

SO3673

hemin ABC transporter (HmuT)

2.20

7.30

13.52

26.71

17.87

19.86

0.91

0.33

0.07

0.06

0.11

0.04

SO3674

hemin ABC transporter, permease protein (HmuU)

1.08

2.53

6.74

11.84

10.57

9.13

1.07

0.49

0.09

0.15

0.47

--

SO3675

hemin ABC transporter, ATP-binding protein (HmuV)

--

4.83

16.36

27.84

21.42

19.39

1.23

0.64

--

0.11

0.41

--

SO3914

TonB-dependent receptor (iron uptake)

2.89

4.45

7.32

--

9.38

11.30

0.74

0.24

0.14

0.05

0.15

0.03

SO4523

iron-regulated outer membrane protein (IrgA)

3.53

5.23

9.19

14.16

23.22

25.92

0.54

0.21

0.08

0.04

0.13

0.04

SO4690

dolichyl-phosphate-mannose-protein mannosyltransferase family protein

1.46

1.45

1.62

2.09

2.16

2.02

1.02

0.71

0.51

0.64

0.48

0.56

SO4743

TonB-dependent receptor

8.12

9.18

7.07

4.48

4.29

3.23

0.66

0.18

0.09

0.08

0.19

0.13

Anaerobic energy metabolism

             

SO0261

heme exporter protein (CcmC)

0.85

--

--

0.26

0.23

0.21

1.24

2.05

1.53

2.81

2.49

2.57

SO0262

heme exporter protein (CcmB)

1.76

1.38

0.79

0.21

0.23

--

--

--

--

--

--

--

SO0263

heme exporter protein (CcmA)

1.01

0.73

0.59

0.12

0.14

0.15

1.45

2.15

2.17

2.63

2.49

3.13

SO0325

dsrE-related protein

0.66

0.56

0.67

0.12

0.08

0.09

1.56

3.36

2.41

2.59

2.64

2.23

SO0398

FAD-binding subunit of inner membrane respiratory complex (FrdA)

1.72

1.74

1.04

0.24

0.23

0.20

0.96

2.14

1.99

2.55

2.03

2.61

SO0403

expressed protein

--

--

--

0.11

0.09

0.12

1.35

2.16

2.46

0.91

1.63

1.27

SO0435

uroporphyrinogen decarboxylase (HemE)

1.27

1.46

0.95

0.32

0.19

0.15

1.50

2.33

2.72

3.64

5.01

5.42

SO0490

transcriptional regulator

--

0.89

0.78

0.08

0.10

--

--

--

--

--

--

--

SO0595

expressed protein

1.04

0.97

0.92

--

0.09

--

--

--

--

--

--

--

SO0975

conserved hypothetical inner membrane protein

1.07

1.15

0.58

0.06

0.06

0.05

1.09

2.02

1.80

4.74

3.06

3.56

SO1250

conserved hypothetical protein

1.02

1.01

0.53

0.15

0.14

0.15

1.20

2.54

3.09

2.14

1.61

1.32

SO1415

transcriptional regulator, TetR family

1.05

0.88

0.57

0.04

0.05

--

--

--

--

--

--

--

SO1522

L-lactate permease, integral IM protein

1.08

0.95

0.70

0.18

0.24

0.15

2.13

3.43

3.33

5.55

4.03

4.27

SO1777

periplasmic decaheme cytochrome c, Fe(III) and Mn(IV) reduction (MtrA)

0.97

--

--

0.11

0.08

0.11

1.64

3.47

4.26

3.19

3.99

5.14

SO1778

decaheme cytochrome c (MtrC)

0.97

1.26

0.69

0.07

0.08

0.06

2.44

6.04

3.47

4.27

3.93

7.85

SO1779

Outer membrane decaheme cytochrome c (OmcA)

1.65

1.93

0.94

0.09

0.07

0.06

2.10

7.04

6.76

8.51

6.91

10.11

SO1910

1,4-dihydroxy-2-naphthoate octaprenyltransferase (MenA)

1.24

1.04

0.71

0.29

0.28

0.22

1.41

2.21

2.22

3.21

2.87

3.29

SO1911

oxidoreductase, short chain dehydrogenase/reductase family

0.71

0.66

0.47

0.03

0.06

0.04

1.90

3.72

2.60

5.44

3.71

3.01

SO2005

dksA-type zinc finger protein

0.46

0.47

0.19

0.05

0.07

--

--

--

--

--

--

--

SO2019

ferrochelatase (HemH 1)

1.33

0.94

0.82

0.18

0.18

0.16

1.29

2.53

2.14

4.77

3.84

5.56

SO2136

aldehyde-alcohol dehydrogenase (AdhE)

0.62

0.41

0.43

0.09

0.11

0.08

2.29

3.05

3.05

7.13

3.75

5.88

SO2834

anaerobic ribonucleoside-triphosphate reductase (NrdD)

1.16

1.83

0.47

0.12

0.09

0.12

0.80

2.27

2.19

2.12

1.55

1.24

SO2865

L-lysine exporter, putative

1.66

1.31

0.70

0.16

0.30

--

--

--

--

--

--

--

SO3119

conserved hypothetical protein

--

--

--

0.19

0.20

0.26

2.18

5.48

2.87

2.11

1.70

2.00

SO3297

transcriptional regulator, LysR family

1.24

0.98

0.72

0.16

0.21

0.29

1.09

0.92

1.08

1.50

1.57

--

SO3416

hypothetical protein

1.13

1.27

0.95

0.24

0.25

0.38

1.77

1.89

2.25

1.05

1.98

1.37

SO3507

conserved hypothetical protein

2.08

1.70

1.45

0.19

0.17

0.10

1.73

--

8.41

3.10

3.00

2.60

SO3553

sulfate permease family protein

0.68

0.74

0.67

0.19

0.17

0.11

2.24

3.94

3.60

7.45

5.47

6.92

SO3627

transcriptional regulator, TetR family

1.17

1.07

0.72

0.03

0.06

0.06

0.92

6.40

3.07

3.19

2.99

1.74

SO3874

transcriptional regulator, LysR family

0.60

0.48

0.30

0.07

0.05

0.05

1.72

4.56

3.75

3.81

2.79

2.96

SO3901

lacZ expression regulator (icc)

1.15

0.75

0.60

0.21

0.20

0.15

1.71

3.61

2.74

3.24

2.23

2.74

SO4138

expressed periplasmic protein

0.95

0.96

0.68

0.13

0.09

0.11

1.42

4.10

2.55

3.76

3.46

3.63

SO4155

sensor histidine kinase for thiosulfate/tetrathionate response (TtrS)

0.72

0.65

0.72

0.10

--

--

--

--

--

--

--

--

SO4157

two component transciptional regulator for thiosulfate/tetrathionate response (TtrR)

0.39

0.66

--

0.12

--

0.09

1.66

2.78

--

1.98

2.02

2.60

SO4204

Sec-independent periplasmic protein translocation protein (TatC)

0.87

0.64

0.61

--

0.27

0.25

1.64

--

1.72

2.53

2.95

3.58

SO4355

cAMP-binding protein

2.73

2.02

1.62

0.19

0.26

0.22

2.01

2.24

1.33

2.44

1.86

2.69

SO4448

molybdenum ABC transporter, periplasmic molybdenum-binding protein (ModA-2)

1.65

1.84

1.00

0.33

0.33

0.43

1.17

1.39

1.28

1.35

1.18

1.06

SO4591

tetraheme cytochrome c (CymA)

--

--

--

0.17

0.15

0.11

2.83

7.01

3.75

3.76

5.27

7.71

SO4623

two component transcriptional regulator

0.68

0.51

0.44

0.11

0.12

0.14

1.21

1.69

1.30

1.31

1.46

1.39

SO4718

two component Sigma54 specific transcriptional regulator for tungstate (molybdate) transport

1.79

1.69

1.42

0.42

0.40

0.47

1.30

1.86

1.83

2.25

2.38

2.82

Protein degradation

             

SO0052

protein export chaperone (SecB)

0.93

1.00

0.68

0.66

2.44

--

--

--

--

--

--

--

SO1126

chaperone protein (DnaK)

0.80

1.14

0.84

0.68

1.79

1.60

0.76

0.95

0.41

0.05

0.06

0.04

SO1127

chaperone protein (DnaJ)

1.19

1.07

0.73

1.00

1.67

1.11

1.22

1.29

0.76

0.23

0.17

0.24

SO2016

heat shock protein (HtpG)

0.88

0.82

0.58

1.15

2.53

1.74

0.93

1.05

0.71

0.10

0.22

0.06

SO2017

Unknown Protein

0.83

0.81

0.56

1.07

2.78

1.64

1.19

0.91

0.61

0.16

0.20

0.14

SO2265

scaffold protein for Fe-S cluster assembly (IscU)

--

1.48

1.33

1.45

4.66

3.74

0.82

0.59

0.36

0.09

0.25

0.19

SO2266

iron recruitment protein (IscA)

1.18

1.28

1.05

1.45

4.46

4.68

1.04

0.81

0.23

0.12

0.25

0.23

SO3588

gpr1/fun34/yaaH family protein

1.09

1.08

1.02

1.39

1.98

2.88

1.20

0.61

0.38

0.44

0.57

0.76

SO4699

oligopeptidase A (PrlC)

0.98

0.92

0.75

1.49

2.36

1.61

1.05

1.08

0.44

0.13

0.28

0.12

  1. Expression ratio values greater than 1 denote increases in gene expression and values between 0 and 1 indicate decreases in gene expression. --: not detected.
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BMC Genomics

ISSN: 1471-2164

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