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Table 3 An across-study comparison of sex- and gonad-biased gene expression in zebrafish

From: A microarray analysis of sex- and gonad-biased gene expression in the zebrafish: Evidence for masculinization of the transcriptome

Gene Name, EST accession number

(if applicable)

Reference

Fold Rank

(This Study)

GCOS Fold

GC-RMA Fold

PMMM Fold

PM Only Fold

Male-enriched Genes

      

anti-Mullerian hormone (amh)

27

18

328.39

154.95

78.09

80.60

cyclin G2 (ccng2)

27

690

328.39

11.78

7.74

8.85

heat shock cognate 70-kd protein (hsp70)

27

-

3.64

2.63

2.20

2.63

similar to septin 4 (sept4)

27

2

608.87

673.38

48.17

364.57

tubulin, alpha 7 like (tuba7l)

27

19

235.72

985.76

46.06

66.53

similar to tektin 1, CO352798

28

3

484.87

681.64

49.65

196.92

dynein, axonemal, intermediate polypeptide 1 (dnai1), CO355627

28

45

144.47

186.74

27.69

50.98

similar to human AKAP-associated sperm protein, CO353327

28

83

58.05

181.15

22.55

44.38

piwi-like 1 (Drosophila) (piwil1), CO354057

28

1261

6.81

8.28

5.12

5.01

similar to testis-specific-A-kinase-anchoring protein, CO354405

28

4

409.79

416.74

58.48

174.20

Female-enriched Genes

      

transmembrane phosphatase with tensin homology (tpte)

27

1084

3.34

4.50

3.30

3.48

RNA binding protein with multiple splicing 2 (rbpms2)

27

216

26.94

48.76

14.73

20.47

connexin 44.2 (cx44.2)

27

139

66.33

198.28

31.92

54.72

SRY-box containing gene 11b (sox11b)

27

187

30.21

79.53

22.06

23.13

cyclin B2 (ccnb2)

27

284

14.58

28.39

12.39

13.34

similar to egg envelope glycoprotein, CO350790

28

132

62.31

190.67

53.93

59.02

flap structure-specific endonuclease 1 (fen1), EV603088

28

-

1.11

1.17

1.10

1.10

hypothetical protein LOC556628, CO350423

28

30

273.38

1679.77

110.57

156.60

B-cell translocation gene 4 (btg4), CO349959

28

75

168.79

416.47

78.66

168.05

similar to transcription factor IIIA, CO349799

28

138

58.00

147.42

40.73

60.90

Testis-upregulated Genes

      

zgc:162225, CO352964

42

139

282.01

121.35

9.68

33.48

WD repeat-containing protein 69, CO355324

42

82

59.34

175.15

21.17

41.71

zgc:158652, CO353149

42

-

113.93

392.11

30.49

42.58

zgc:112008, CO352835

42

176

28.11

111.65

13.66

24.40

similar to CG14551-PA, CO352954

42

9

301.99

280.30

46.03

207.76

hypothetical protein LOC558005, CO355049

28

147

69.83

220.63

24.25

14.03

unknown transcript, CO355999

28

383

12.96

9.27

12.50

56.80

hypothetical protein LOC100003104, CO353145

28

13

165.59

1010.46

42.16

81.04

similar to polyprotein, CO355597

28

63

51.37

131.92

47.53

48.39

similar to tektin 1, CO353325

28

12

167.65

848.47

57.56

69.06

Ovary-upregulated Genes

      

hypothetical protein LOC100001369, CO350972

42

-

3.45

3.29

2.22

2.44

hypothetical protein LOC555929, CO351149

42

-

2.66

5.13

2.19

3.21

similar to novel rhamnose binding lectin, CO350303

42

-

1.17

1.21

1.14

1.20

unknown transcript, CO350393

42

-

2.03

2.79

1.88

1.97

similar to egg envelope glycoprotein, CO350790

28

-

1.37

1.92

1.48

1.52

wu:fi40a06, CO349940

28

-

1.26

1.93

1.48

1.49

DEAD (Asp-Glu-Ala-Asp) box polypeptide 56, CO354027

28

810

2.38

2.47

1.60

1.58

hypothetical protein LOC447813, CO350110

28

-

2.02

1.76

1.02

1.02

clone MGC:55720, CO350755

28

909

2.13

2.37

1.35

1.35

retinol saturase like (retsatl), CO350808

28

-

1.75

2.49

1.79

1.85

  1. List of sex- and gonad-biased genes identified by other recent zebrafish studies [27, 28, 42]. The sex-biased genes are based on testis-ovary comparisons, as in our study. These genes were chosen from the above studies based on reportedly high expression bias. We screened our lists of differentially expressed genes to assess agreement with the other studies. The "fold rank" is the position each gene occupies in our lists, based on the mean of rank across the four absolute expression comparisons. sept4, for example, is the gene demonstrating the second-highest male-enriched expression (out of 3387 total male-enriched genes). No rank is listed if the gene failed to pass our "strict consensus" statistical criteria (see Methods). Also listed are fold change estimates corresponding to each of the four absolute expression analyses.
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BMC Genomics

ISSN: 1471-2164

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