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Table 5 Consistency of selected gene expression differences among independent experiments, measured by qRT-PCR and/or microarray.

From: Infection and genotype remodel the entire soybean transcriptome

    

Pilot experiment

 

72-replicate experiment (array)

 
    

5 day

 

5 day (average upper and lower versus mock)

 

Geno-typea

Gene IDb

Annotationc

Inoc/Mock

qRT

array

Wholef

Subg A

Sub B

Sub C

Sub D

Sub E

Sub F

V71-370

Gma.441.1.S1_at

Ubiquitin (AtRUB1) [HK]

meand

1.17

1.08

1.07

1.08

1.04

1.05

1.21

1.09

-1.01

   

s.e.e

0.9

0.08

0.03

0.09

0.05

0.08

0.08

0.04

0.09

 

Gma.16125.1.S1_s_at

Ribosomal protein S27-like [HK]

mean

1.12

1.16

1.15‡

1.17

1.19

1.14

1.16

1.19

1.08

   

s.e.

0.15

0.14

0.06

0.10

0.12

0.14

0.16

0.12

0.11

 

GmaAffx.90824.1.S1_s_at

26S proteasome subunit RPN2a [HK]

mean

-1.25

-1.16

-1.08

-1.00

-1.23

-1.08

-1.12

1.00

-1.02

   

s.e.

0.18

0.15

0.04

0.10

0.08

0.09

0.08

0.06

0.08

 

GmaAffx.90181.1.A1_at

Actin

mean

2.0

1.25

-1.03

1.07

-1.00

-1.11

1.07

-1.11

-1.05

   

s.e.

0.8

0.5

0.07

0.17

0.17

0.20

0.17

0.16

0.16

 

GmaAffx.60616.1.S1_at

Hcr9-OR2A

mean

-1.7

-1.5

-1.35‡

-1.28

-1.31

-1.20

-1.20

-1.37

-1.8

   

s.e.

0.49

0.22

0.04

0.10

0.11

0.12

0.09

0.10

0.09

 

Gma.447.1.S1_at

Defense associated acid phosphatase

mean

-2.8

-1.47

-1.9‡

-1.34

-1.34

-2.9

-1.5

-2.8

-1.9

   

s.e.

0.40

0.27

0.05

0.18

0.23

0.06

0.16

0.06

0.11

 

GmaAffx.64261.1.A1_at

Quinone oxidoreductase

mean

3.6

8.5*‡

5.6‡

5.3

5.4

5.3

7.4

4.4

7.2

   

s.e.

0.7

2.7

0.6

1.8

1.3

1.1

1.9

0.9

1.7

 

Gma.6640.1.S1_at

At5g66390 (secretory peroxidase)

mean

1.5

1.46‡

1.07‡

1.06

1.15

-1.10

1.10

1.11

1.11

   

s.e.

0.43

0.10

0.05

0.12

0.11

0.10

0.11

0.09

0.13

 

GmaAffx.18905.1.S1_at

Cell death associated protein

mean

2.5

2.4‡

2.3‡

2.0

1.9

2.7

2.8

2.4

2.4

   

s.e.

0.41

0.7

0.21

0.42

0.42

0.6

0.46

0.46

0.37

 

Gma.17993.1.S1_at

P21 protein

mean

60

70‡

30‡

29

34

26

40

36

24

   

s.e.

13

19

3.7

11

9

7

7

10

9

 

GmaAffx.75675.1.A1_at

Phenylalanine ammonia-lyase

mean

3.9

7.6*‡

4.4‡

4.4

4.4

4.7

4.0

4.6

4.9

   

s.e.

0.41

0.9

0.29

0.9

0.7

0.7

0.46

0.7

0.7

 

GmaAffx.2799.1.A1_at

NtPRp27-like protein

mean

12

20‡

7.8‡

5.9

7.8

8.0

7.8

9.6

8.3

   

s.e.

0.6

5

0.6

1.4

1.4

1.1

0.9

1.2

1.3

 

Gma.16733.2.S1_at

WRKY4 transcription factor

mean

4.9

6.8‡

2.9‡

3.9

3.5

2.6

3.1

2.9

2.6

   

s.e.

0.6

1.7

0.37

1.0

1.2

0.8

0.9

1.1

0.7

 

GmaAffx.29692.1.S1_at

Chitinase (class II)

mean

1.9

2.9‡

2.0‡

2.4

2.1

1.6

1.9

1.8

2.2

   

s.e.

0.47

0.7

0.11

0.34

0.27

0.22

0.20

0.29

0.23

 

Gma.16911.1.S1_at

Cytochrome P450 family protein

mean

-1.23

1.6

1.24‡

1.07

1.20

1.29

1.21

1.28

1.47

   

s.e.

0.26

0.33

0.05

0.11

0.11

0.11

0.11

0.10

0.08

 

GmaAffx.7209.1.A1_at

UDP-glucose 6-dehydrogenase

mean

-1.02

1.36

-1.02

1.09

1.17

-1.05

-1.03

-1.24

-1.01

   

s.e.

0.10

0.21

0.07

0.14

0.22

0.11

0.13

0.13

0.15

 

GmaAffx.47171.1.A1_at

Putative resistance protein

mean

-1.03

1.43‡

1.6‡

1.35

1.5

1.5

1.6

1.7

1.9

   

s.e.

0.12

0.38

0.08

0.17

0.17

0.21

0.16

0.16

0.19

 

Gma.3473.1.S1_at

Protein, small heat shock

mean

-1.26

-1.20

-1.7‡

1.7

-1.6

-3.4

-1.7

-2.1

-2.3

   

s.e.

0.26

0.22

0.06

0.30

0.16

0.08

0.14

0.11

0.08

 

GmaAffx.90984.1.A1_at

Germin-like protein

mean

14

5.7‡

2.1‡

2.0

2.2

1.9

1.9

2.0

2.4

   

s.e.

2.5

2.2

0.16

0.35

0.44

0.31

0.33

0.47

0.39

 

GmaAffx.32612.1.S1_at

HI4'OMT

mean

18

24‡

14‡

9.6a

8.9a

20b

12a

21b

22b

   

s.e.

1.8

6.5

1.5

3.2

2.3

3.3

2.8

4.7

6

 

GmaAffx.90059.1.S1_at

HcrVf2 protein

mean

7.4

3.7‡

3.0‡

3.2

2.7

2.9

3.2

2.9

3.2

   

s.e.

2.0

0.8

0.22

0.5

0.37

0.26

0.41

0.42

0.8

 

GmaAffx.79817.1.S1_at

SGT1

mean

1.13

1.04

-1.01

1.07

-1.10

1.00

-1.04

-1.11

1.13

   

s.e.

0.14

0.07

0.04

0.15

0.08

0.14

0.06

0.05

0.07

Sloan

Gma.441.1.S1_at

Ubiquitin (AtRUB1) [HK]

meand

-1.04

1.19

1.12‡

1.07

1.20

1.07

1.23

1.10

1.08

   

s.e.e

0.10

0.14

0.04

0.09

0.06

0.09

0.12

0.08

0.11

 

Gma.16125.1.S1_s_at

Ribosomal protein S27-like [HK]

mean

-1.18

1.03

-1.07

1.02

-1.04

-1.14

1.10

-1.17

-1.14

   

s.e.

0.5

0.18

0.06

0.08

0.06

0.15

0.22

0.07

0.10

 

GmaAffx.90824.1.S1_s_at

26S proteasome subunit RPN2a [HK]

mean

1.5

1.01

-1.06‡

-1.15

-1.03

-1.01

-1.06

-1.03

-1.07

   

s.e.

0.20

0.11

0.04

0.09

0.06

0.13

0.09

0.06

0.04

 

GmaAffx.90181.1.A1_at

Actin

mean

-1.36

1.49‡

-1.19‡

-1.29

-1.18

-1.28

-1.13

-1.33

1.10

   

s.e.

0.26

0.40

0.06

0.10

0.22

0.16

0.12

0.13

0.22

 

GmaAffx.60616.1.S1_at

Hcr9-OR2A

mean

-1.7

-2.2‡

-1.9‡

-1.45

-1.8

-2.0

-1.9

-1.7

-2.3

   

s.e.

0.41

0.12

0.05

0.12

0.09

0.14

0.09

0.12

0.08

 

Gma.447.1.S1_at

Defense associated acid phosphatase

mean

-1.43

-1.47

-1.8‡

-1.8

-1.6

-2.0

-1.8

-2.2

-1.48

   

s.e.

0.14

0.21

0.06

0.15

0.12

0.17

0.13

0.09

0.17

 

GmaAffx.64261.1.A1_at

Quinone oxidoreductase

mean

3.1

2.3‡

2.6‡

3.9

4.7

-1.24

2.7

3.0

3.0

   

s.e.

0.6

0.40

0.39

1.5

1.5

0.23

0.8

1.1

1.1

 

Gma.6640.1.S1_at

At5g66390 (secretory peroxidase)

mean

1.14

-1.08

-1.16‡

-1.38

-1.21

-1.20

1.30

-1.10

-1.33

   

s.e.

0.49

0.22

0.06

0.15

0.10

0.15

0.16

0.17

0.13

 

GmaAffx.18905.1.S1_at

Cell death associated protein

mean

3.4

1.5‡

2.9†‡

3.5

4.5

2.1

3.2

2.9

2.2

   

s.e.

0.5

0.32

0.27

0.9

0.7

0.5

0.7

0.6

0.39

 

Gma.17993.1.S1_at

P21 protein

mean

72

94‡

43a‡

41a

45a

44a

21b

100c

55a

   

s.e.

27

27

7

18

20

16

9

24

17

 

GmaAffx.75675.1.A1_at

Phenylalanine ammonia-lyase

mean

9.3

15‡

6.3‡

7.2

7.7

6.0

4.4

7.2

6.2

   

s.e.

2.8

2.7

0.44

1.3

1.2

1.1

0.40

1.5

0.7

 

GmaAffx.2799.1.A1_at

NtPRp27-like protein

mean

14

15‡

8.3‡

5.8

8.6

9.8

6.0

11

11

   

s.e.

2.4

3.4

0.7

0.8

1.5

1.9

1.0

2.5

1.9

 

Gma.16733.2.S1_at

WRKY4 transcription factor

mean

5.8

5.3‡

3.5‡

6.9

3.8

2.7

4.3

3.1

2.3

   

s.e.

1.3

1.2

0.44

2.2

1.1

0.8

1.1

1.1

0.5

 

GmaAffx.29692.1.S1_at

Chitinase (class II)

mean

2.5

2.7‡

3.1‡

3.2

2.7

2.7

2.9

3.5

4.2

   

s.e.

0.35

0.6

0.21

0.6

0.34

0.6

0.27

0.7

0.5

 

Gma.16911.1.S1_at

Cytochrome P450 family protein

mean

3.4

4.0‡

3.1‡

2.9

3.4

2.9

2.8

4.2

3.0

   

s.e.

0.8

1.0

0.18

0.5

0.37

0.40

0.28

0.46

0.44

 

GmaAffx.7209.1.A1_at

UDP-glucose 6-dehydrogenase

mean

1.8

2.2‡

1.02

1.49

1.28

-1.7

-1.08

1.16

1.04

   

s.e.

0.27

0.6

0.11

0.21

0.28

0.12

0.14

0.31

0.26

 

GmaAffx.47171.1.A1_at

Putative resistance protein

mean

-1.07

1.08

1.21‡

1.23

1.18

1.11

1.16

1.35

1.30

   

s.e.

0.16

0.34

0.07

0.18

0.15

0.16

0.14

0.18

0.17

 

Gma.3473.1.S1_at

Protein, small heat shock

mean

-1.41

-1.6

-2.2‡

1.03

-3.6

-3.3

-1.9

-2.4

-1.9

   

s.e.

0.16

0.09

0.05

0.37

0.05

0.08

0.08

0.11

0.15

 

GmaAffx.90984.1.A1_at

Germin-like protein

mean

5.3

2.5‡

-1.06

1.10

1.18

-1.18

-1.06

-1.12

-1.23

   

s.e.

1.7

0.5

0.07

0.20

0.21

0.12

0.10

0.10

0.14

 

GmaAffx.32612.1.S1_at

HI4'OMT

mean

57

16‡

25a‡

18a

22a

24a

18a

43b

41b

   

s.e.

16

4.2

2.8

6

5

7

4.9

12

8

 

GmaAffx.90059.1.S1_at

HcrVf2 protein

mean

3.9

2.5‡

2.7‡

5.5

4.0

1.3

2.3

2.8

2.4

   

s.e.

1.1

0.38

0.25

0.8

0.7

0.17

0.35

0.44

0.7

 

GmaAffx.79817.1.S1_at

SGT1

mean

1.21

-1.19

-1.04

1.08

-1.02

1.01

-1.02

-1.08

-1.18

   

s.e.

0.28

0.05

0.05

0.18

0.06

0.20

0.07

0.05

0.04

  1. aGenotypes used for this comparison were cultivars V71-370 and Sloan; b22 genes selected for qRT assays. cThe functional annotation of the selected genes. [HK] indicates housekeeping genes used to normalize the qRT-PCR results dThe average expression difference between inoculated and mock samples, calculated as a fold-change. Negative values indicate downward change in response to infection. The presence of letter suffixes (a, b, c) after mean values indicates the presence of significant variation among the subgroup means, as determined by Least Significant Difference with a cutoff of an FDR-adjusted p value of 0.05. In those cases, means with the same suffix are not significantly different from one another. If no suffixes are present, there are no significant differences among any of the means. Symbol * indicates gene expression differences measured by microarray analysis in the pilot experiment that differ significantly from the measurements obtained by qRT-PCR analysis, determined using t tests with a cutoff of an FDR-adjusted p value of 0.05. Symbol † indicates gene expression differences measured by microarray analysis in the whole 72 replicate experiment that differ significantly from the measurements obtained by microarray analysis in the pilot experiment, determined using t tests with a cutoff of an FDR-adjusted p value of 0.05. Symbol ‡ indicates expression changes in the pilot microarray experiment and the whole 72 replicate experiment that are significant at a cutoff of a TST-FDR-adjusted p value of 0.01. eThe standard errors are calculated from log-transformed expression differences from 3 technical replicates in the case of the qRT-PCR results, from 4 biological replicates in the case of the pilot array data, from 72 biological replicates in the whole main experiment, and from 12 biological replicates in the main experiment sub-groups. fAll the 72-replicates as a whole experiment. gSub-groups of the whole experiment each comprising 12 consecutive replicates.
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BMC Genomics

ISSN: 1471-2164

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