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Table 4 Biological comparisons. Expression of genes in ethylene biosynthesis and signal transduction cascade as calculated with six different methods. Numbers in brackets after a gene name show how many genes of a family are on the microarray, followed by the size of the family. Expression data of a gene family is the summation of expression of the individual gene members. The columns with a p showing the significance of the fold change ('x' columns) between air control and ethylene (eth) treated plants. ns = not significant * = p < 0.05, ** = p < 0.01, *** = p < 0.001.

From: How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results

 

MAS 5.0

dChip PMMM

dChip PM

  

gene

Air

eth

p

x

Air

eth

p

X

Air

eth

p

x

ACC synthase (10/11)

378

339

ns

-

1882

1760

*

0.9

2489

2373

ns

-

ACC oxidase (10/10)

2960

5845

**

2.0

6196

12866

**

2.1

8301

16931

***

2.0

Receptors (5/5)

327

932

**

2.9

806

2104

**

2.6

1331

2881

***

2.2

CTR1

55

242

***

4.4

120

614

***

5.1

278

877

***

3.1

EIN2

191

182

ns

-

429

415

ns

-

588

558

ns

-

EIN3/EIL (4/4)

578

652

**

1.1

1464

1714

**

1.2

2075

2377

**

1.1

 

RMA

PDNN

GC-RMA

  

gene

Air

eth

p

x

Air

eth

p

X

Air

eth

p

x

ACC synthase (10/11)

1304

1186

ns

-

4337

4057

*

0.9

801

567

***

0.7

ACC oxidase (10/10)

7341

15768

***

2.2

14731

28773

***

2.0

9116

23075

***

2.5

Receptors (5/5)

869

2150

***

2.5

2419

5059

***

2.1

600

2221

***

3.7

CTR1

210

904

***

4.3

558

1566

***

2.8

140

1031

***

7.4

EIN2

608

563

ns

-

1029

974

ns

 

407

369

ns

0.9

EIN3/EIL (4/4)

1493

1740

***

1.2

3678

4416

*

1.2

1785

2207

***

1.2