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Table 2 The 49 annotated candidate reference genes ranked in order of their coefficient of variation (spot: location on microarray, ID genbank: accession number, stdev: standard deviation, description: best BLAST hit description as described in GigasDatabase, e value: best BLAST hit e-value, CV: coefficient of variation, max: maximum value, min: minimum value, MFC: maximum fold change, p value: one-way ANOVA P > 0.05)

From: Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns

RANK

spot

ID genebank

description (GigasDatabase)

e value

MEAN

stdev

CV

max

min

MFC

p value

2

24202

BQ426480

(sp:Q66KU2) Protein transport protein Sec61 subunit gamma OS = Xenopus laevis GN = sec61g PE = 3 SV = 1

7E-20

6.16

0.07

0.012

6.32

6.01

1.05

0.28

4

8432

BQ427048

(sp:P61210) ADP-ribosylation factor 1 OS = Locusta migratoria GN = ARF1 PE = 2 SV = 2

2E-92

5.82

0.08

0.014

5.98

5.61

1.07

0.13

5

4341

FP005681

(sp:Q80TM9) Nischarin OS = Mus musculus GN = Nisch PE = 1 SV = 2

2E-17

5.28

0.07

0.014

5.42

5.14

1.05

0.18

7

9190

AM856720

(sp:Q3SXD3) HD domain-containing protein 2 OS = Mus musculus GN = Hddc2 PE = 2 SV = 1

5E-59

4.04

0.06

0.014

4.16

3.93

1.06

0.39

12

4953

FP007578

(sp:P55260) Annexin A4 OS = Rattus norvegicus GN = Anxa4 PE = 1 SV = 3

3E-24

5.80

0.09

0.015

5.99

5.64

1.06

0.05

17

3774

EW777430

(sp:Q80ZA5) Sodium-driven chloride bicarbonate exchanger OS = Rattus norvegicus GN = Slc4a10 PE = 2 SV = 1

2E-87

5.57

0.09

0.016

5.78

5.39

1.07

0.22

18

16231

AM867010

(sp:Q6PDY2) 2-aminoethanethiol dioxygenase OS = Mus musculus GN = Ado PE = 1 SV = 2

3E-24

4.68

0.07

0.016

4.84

4.55

1.06

0.37

23

24189

AM862676

(sp:P49756) RNA-binding protein 25 OS = Homo sapiens GN = RBM25 PE = 1 SV = 3

8E-38

5.17

0.08

0.016

5.31

4.97

1.07

0.11

25

21853

AM867442

(sp:Q9CSV6) Vesicle transport protein SFT2C OS = Mus musculus GN = Sft2d3 PE = 2 SV = 2

8E-17

4.92

0.08

0.016

5.08

4.74

1.07

0.08

29

21268

FP007036

(sp:Q5RE10) Protein TSSC1 OS = Pongo abelii GN = TSSC1 PE = 2 SV = 1

7E-93

5.26

0.09

0.017

5.52

5.09

1.08

0.06

31

2316

FP004268

Branchiostoma floridae hypothetical protein (BRAFLDRAFT_123626) mRNA, complete cds

6E-11

5.72

0.10

0.017

5.96

5.46

1.09

0.18

35

27321

CU998396

(sp:Q5U5C5) U4/U6 small nuclear ribonucleoprotein Prp31 OS = Xenopus laevis GN = prpf31 PE = 2 SV = 1

2E-42

5.49

0.10

0.018

5.70

5.32

1.07

0.09

36

14581

CU682778

(sp:Q96ME1) F-box/LRR-repeat protein 18 OS = Homo sapiens GN = FBXL18 PE = 2 SV = 2

4E-13

4.67

0.09

0.018

4.97

4.53

1.10

0.12

39

38790

FP007991

(sp:Q8IY22) C-Maf-inducing protein OS = Homo sapiens GN = CMIP PE = 1 SV = 2

2E-62

5.54

0.10

0.019

5.73

5.32

1.08

0.31

43

17127

CU994599

(sp:O16099) Maltase 2 OS = Drosophila virilis GN = Mav2 PE = 3 SV = 1

6E-15

6.04

0.11

0.019

6.29

5.84

1.08

0.08

44

38094

AM854363

(sp:P49790) Nuclear pore complex protein Nup153 OS = Homo sapiens GN = NUP153 PE = 1 SV = 2

1E-06

5.36

0.10

0.019

5.52

5.13

1.08

0.35

45

42336

AM867367

(sp:Q9V8K2) Exocyst complex component 3 OS = Drosophila melanogaster GN = sec6 PE = 1 SV = 2

2E-46

4.07

0.08

0.019

4.24

3.90

1.09

0.51

48

18292

AM857903

(sp:Q9HBH5) Retinol dehydrogenase 14 OS = Homo sapiens GN = RDH14 PE = 1 SV = 1

1E-52

4.86

0.09

0.019

5.06

4.69

1.08

0.98

50

23889

AM857691

(sp:Q53HI1) Protein unc-50 homolog OS = Homo sapiens GN = UNC50 PE = 1 SV = 2

1E-44

4.94

0.10

0.019

5.19

4.73

1.10

0.14

51

9261

CB617377

(sp:P35980) 60S ribosomal protein L18 OS = Mus musculus GN = Rpl18 PE = 2 SV = 3

3E-52

5.62

0.11

0.019

5.88

5.41

1.09

0.12

57

6325

AM854187

(sp:Q8BI36) JNK1/MAPK8-associated membrane protein OS = Mus musculus GN = Jkamp PE = 1 SV = 2

4E-54

4.06

0.08

0.020

4.23

3.90

1.08

0.97

59

26590

CU991951

(sp:O75592) Probable E3 ubiquitin-protein ligase MYCBP2 OS = Homo sapiens GN = MYCBP2 PE = 1 SV = 3

1E-93

5.48

0.11

0.020

5.70

5.24

1.09

0.06

63

14888

CU999965

(sp:Q99323) Myosin heavy chain, non-muscle OS = Drosophila melanogaster GN = zip PE = 1 SV = 2

4E-61

5.47

0.11

0.020

5.66

5.25

1.08

0.06

65

28114

AM865894

(sp:Q297U0) Death domain-containing adapter protein BG4 OS = Drosophila pseudoobscura pseudoobscura GN = BG4 PE = 3 SV = 2

9E-06

5.41

0.11

0.020

5.59

5.19

1.08

0.15

71

25525

FP001776

(sp:P38935) DNA-binding protein SMUBP-2 OS = Homo sapiens GN = IGHMBP2 PE = 1 SV = 2

3E-22

4.90

0.10

0.021

5.13

4.72

1.09

0.05

72

31850

AM859152

hypothetical protein [Leishmania infantum]

7E-06

4.51

0.09

0.021

4.65

4.27

1.09

0.08

73

11422

AM857565

(sp:O75689) Arf-GAP with dual PH domain-containing protein 1 OS = Homo sapiens GN = ADAP1 PE = 1 SV = 2

2E-90

5.78

0.12

0.021

6.04

5.51

1.10

0.21

74

9287

AM858936

(sp:O75970) Multiple PDZ domain protein OS = Homo sapiens GN = MPDZ PE = 1 SV = 1

2E-54

4.01

0.08

0.021

4.16

3.84

1.08

0.26

76

12345

FP002886

(sp:Q9UP83) Conserved oligomeric Golgi complex subunit 5 OS = Homo sapiens GN = COG5 PE = 1 SV = 2

1E-40

5.12

0.11

0.021

5.46

4.98

1.10

0.15

77

16551

AM854998

(sp:P34384) Uncharacterized protein F02A9.4b OS = Caenorhabditis elegans GN = F02A9.4 PE = 2 SV = 3

6E-16

4.88

0.10

0.021

5.13

4.71

1.09

0.07

78

37299

AM854324

(sp:O14681) Etoposide-induced protein 2.4 homolog OS = Homo sapiens GN = EI24 PE = 1 SV = 4

3E-46

4.34

0.09

0.021

4.54

4.20

1.08

0.12

79

44361

AM867088

hypothetical protein LOC100216081 [Xenopus (Silurana) tropicalis]

8E-07

4.03

0.09

0.021

4.22

3.90

1.08

0.43

82

4930

CX069207

(sp:P24392) Peroxisome assembly factor 1 OS = Rattus norvegicus GN = Pxmp3 PE = 2 SV = 1

1E-14

4.24

0.09

0.022

4.42

4.03

1.10

0.49

83

23819

DW713831

(sp:Q8R107) PRELI domain-containing protein 1, mitochondrial OS = Mus musculus GN = Prelid1 PE = 2 SV = 1

5E-31

4.31

0.09

0.022

4.45

4.13

1.08

0.28

88

42190

CU999658

(sp:Q4R4P4) Fatty acid 2-hydroxylase OS = Macaca fascicularis GN = FA2H PE = 2 SV = 1

2E-37

4.93

0.11

0.022

5.09

4.69

1.09

0.13

90

41203

AM861170

(sp:O95562) Vesicle transport protein SFT2B OS = Homo sapiens GN = SFT2D2 PE = 1 SV = 1

2E-45

4.67

0.10

0.022

4.92

4.50

1.09

0.39

92

28026

FP003987

(sp:P28668) Bifunctional aminoacyl-tRNA synthetase OS = Drosophila melanogaster GN = Aats-glupro PE = 1 SV = 2

9E-26

5.45

0.12

0.023

5.76

5.24

1.10

0.34

96

28299

AM860951

(sp:Q63055) ADP-ribosylation factor-related protein 1 OS = Rattus norvegicus GN = Arfrp1 PE = 2 SV = 1

3E-61

4.58

0.10

0.023

4.77

4.34

1.10

0.42

99

1305

CU987227

(sp:O75533) Splicing factor 3B subunit 1 OS = Homo sapiens GN = SF3B1 PE = 1 SV = 3

5E-39

4.04

0.09

0.023

4.21

3.90

1.08

0.42

101

19889

FP003031

(sp:A1Z623) 15 kDa selenoprotein OS = Sus scrofa GN = SEP15 PE = 2 SV = 2

2E-27

5.58

0.13

0.023

5.86

5.34

1.10

0.08

102

31829

CX739641

(sp:P06603) Tubulin alpha-1 chain OS = Drosophila melanogaster GN = alphaTub84B PE = 2 SV = 1

1E-173

6.28

0.15

0.024

6.57

5.99

1.10

0.07

106

27419

FP004307

(sp:Q7KHA1) Phosphoglucomutase OS = Drosophila simulans GN = Pgm PE = 3 SV = 1

2E-08

4.40

0.11

0.024

4.61

4.23

1.09

0.26

109

9265

CB617357

(sp:P62925) Eukaryotic translation initiation factor 5A OS = Spodoptera frugiperda GN = eIF-5A PE = 2 SV = 1

9E-52

5.63

0.14

0.024

5.91

5.42

1.09

0.31

112

19642

AM859051

(sp:Q5RAK3) RING finger protein 180 OS = Pongo abelii GN = RNF180 PE = 2 SV = 1

2E-08

4.47

0.11

0.024

4.69

4.30

1.09

0.11

113

41799

AM855515

(sp:Q6GMK8) Mannose-1-phosphate guanyltransferase alpha-A OS = Danio rerio GN = gmppaa PE = 2 SV = 1

1E-119

4.62

0.11

0.024

4.82

4.40

1.10

0.24

121

12762

FP001461

(sp:Q9EPS3) D-glucuronyl C5-epimerase OS = Mus musculus GN = Glce PE = 1 SV = 1

1E-19

4.96

0.13

0.026

5.19

4.76

1.09

0.13

122

43827

FP002120

(sp:Q3SZV2) UPF0459 protein C19orf50 homolog OS = Bos taurus PE = 2 SV = 1

9E-21

4.66

0.12

0.026

4.86

4.42

1.10

0.09

124

30267

CX069057

(sp:Q5R9Z1) Vacuolar protein sorting-associated protein 29 OS = Pongo abelii GN = VPS29 PE = 2 SV = 1

5E-93

5.58

0.15

0.028

5.84

5.34

1.09

0.06

125

14686

AM862926

(sp:Q3TEA8) Heterochromatin protein 1-binding protein 3 OS = Mus musculus GN = Hp1bp3 PE = 1 SV = 1

4E-14

4.89

0.13

0.028

5.16

4.69

1.10

0.10

  1. CV indicates the coefficient of variation and equals the standard deviation divided by the mean. MFC indicates the maximum fold change, i.e., the ratio of the maximum and minimum values observed within the dataset.
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