Table 2

Cadmium regulated microarray elements

Up-regulated elements

Siga

Seqb

EST Cluster

M averagec

A averagec

Hit Description

P Valued

Putative GO annotations


8

9

Contig 262

1.02 ± 0.31

10.12 ± 1.88

2-domain hemoglobin protein subunit

< 0.001

GO:0015671, GO:0005833, GO:0005344

2

16

Contig 272

0.43 ± 0.21

9.06 ± 1.50

CG30045-PA

< 0.001

GO:0042302

1

1

Singlet 433

0.71

12.08

CG6305-PA

0.062

GO:0042302

1

1

Singlet 498

1.02

9.15

chitinase-1

0.028

GO:0008061, GO:0006030, GO:0004568, GO:0005576

3

4

Contig 213

0.82 ± 0.12

9.07 ± 0.53

chitinase-2

< 0.001

GO:0008061, GO:0006030, GO:0004568, GO:0005576

1

3

Contig 218

0.93 ± 0.19

9.64 ± 1.77

chitotriosidase

0.005

GO:0008061, GO:0006030, GO:0016798, GO:0005576

1

3

Contig 209

0.41 ± 0.17

12.21 ± 1.48

CUO6 BLACRCuticle protein 6 (BcNCP14.9)

0.06

GO:0042302

4

6

Contig 241

1.07 ± 0.31

10.76 ± 2.07

cuticle protein-1

0.018

GO:0042302

5

8

Contig 257

1.03 ± 0.33

9.96 ± 1.54

cuticle protein-2

< 0.001

GO:0042302

13

28

Contig 273

0.91 ± 0.32

10.05 ± 1.65

cuticle protein-3

< 0.001

GO:0042302

1

3

Contig 149

0.72 ± 0.28

8.55 ± 0.92

cuticle protein-4

0.011

GO:0042302

5

8

Contig 261

0.88 ± 0.30

9.87 ± 1.42

cuticle protein-5

< 0.001

GO:0042302

1

1

Singlet 15

1.23

14.06

ERGA6350

0.009

1

1

Singlet 469

0.80

7.99

helix-loop-helix transcription factor

0.055

GO:0006355, GO:0003677

1

1

Contig 21

1.45

10.03

hemoglobin-1

0.003

GO:0015671, GO:0005833, GO:0005344

1

1

Contig 16

1.08

9.81

hemoglobin-2

< 0.001

GO:0015671, GO:0005833, GO:0005344

1

1

Singlet 65

2.16

8.34

Hypothetical protein CBG14247

< 0.001

4

4

Contig 221

1.98 ± 0.47

8.88 ± 0.82

Metallothionein

< 0.001

GO:0046872, GO:0006875

1

5

Contig 220

0.31 ± 0.49

8.95 ± 0.62

myosin 2 light chain

0.08

GO:0005509

2

4

Contig 227

0.70 ± 0.04

12.59 ± 2.37

OPSC1 HEMSACompound eye opsin BCRH1

0.036

GO:0007602, GO:0016021, GO:0001584, GO:0007186

1

1

Singlet 251

1.18

10.90

PREDICTED: similar to chitinase

0.019

GO:0008061, GO:0006030, GO:0016798, GO:0005576

1

1

Singlet 459

1.15

7.42

PREDICTED: similar to glutathione S-transferase

0.021

GO:0016740

1

1

Singlet 1

1.94

8.99

Unknown EST-1

0.009

3

3

Contig 232

1.14 ± 037

8.27 ± 0.99

Unknown EST-2

< 0.001

7

8

Contig 253

1.05 ± 0.44

9.99 ± 1.38

Unknown EST-3

< 0.001

1

1

Singlet 166

0.87

8.20

Unknown EST-4

0.048

1

1

Singlet 64

0.75

9.95

Unknown EST-5

0.059

1

1

Singlet 49

0.74

8.77

Unknown EST-6

0.067

1

5

Contig 237

0.33 ± 0.21

10.11 ± 1.55

Unknown EST-7

0.073

1

1

Singlet 172

0.68

8.23

Unknown EST-8

0.071

24

Unsequenced


Down-regulated elements

Siga

Seqb

EST Cluster

M averagec

A averagec

Hit Description

P Valued

Putative GO annotations


1

2

Contig 135

-0.36 ± 0.66

9.28 ± 0.08

carboxypeptidase A1

0.068

GO:0006508, GO:0004182

1

1

Singlet 97

-1.04

6.94

endo-1,4-mannanase

0.009

GO:0016985, GO:0000272

1

3

Contig 202

-0.38 ± 0.36

8.39 ± 1.02

PREDICTED: similar to CG31997-PA

0.036

2

2

Contig 83

-1.29 ± 0.06

8.00 ± 0.40

PREDICTED: similar to monooxygenase

0.001

1

3

Contig 162

-0.37 ± 0.30

8.98 ± 1.04

ribosomal protein S11-2

0.02

GO:0006412, GO:0003735, GO:0005840

1

2

Contig 191

-0.61 ± 0.27

10.76 ± 3.35

Unknown EST-1

0.019

2

4

Contig 212

-0.72 ± 0.38

8.77 ± 0.97

Unknown EST-2

< 0.001

4

5

Contig 229

-1.32 ± 0.11

9.96 ± 0.90

Unknown EST-3

< 0.001

4

7

Contig 249

-1.08 ± 0.27

8.13 ± 0.98

Unknown EST-4

< 0.001

1

2

Contig 56

-0.41 ± 0.36

9.25 ± 0.99

Unknown EST-5

0.056

1

1

Contig 71

-0.71

6.21

Unknown EST-6

0.027

1

1

Singlet 79

-1.08

8.90

Unknown EST-7

0.014

10

Unsequenced


aNumber of microarray elements determined to be significant on the array using the empirical Bayes method to shrink the gene-wise error estimate in cadmium treated vs. control Daphnia pulex (P < 0.05). control Daphnia pulex (P ≤ 0.05).

bNumber of microarray elements selected for sequencing based on cadmium response determined in the current study; Eads et al., in review; and Colbourne et al., in review.

cMean value (± SD) based on all sequenced microarray elements.

dPermutation tests were performed for clones sharing common putative annotations. These tests included 1000 simulations using the mean expression values to determine the Probability of obtaining the M average for an EST cluster.

Shaw et al. BMC Genomics 2007 8:477   doi:10.1186/1471-2164-8-477

Open Data