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Table 3 Highest expressed protein-coding genes in late first trimester placenta

From: Sex differences in the late first trimester human placenta transcriptome

#

Gene symbol

Chr

Description

TPM highest in placenta?a

Placenta specific?b

Where else expressed?b

Upregulated in first vs termc

1

KISS1

1

KiSS-1 metastasis-suppressor

+ + +

N

 

Term

2

CGA

6

Glycoprotein hormones, alpha polypeptide

N

N

  

3

TFPI2

7

Tissue factor pathway inhibitor 2

N

N

  

4

CSH1

17

Chorionic somatomammotropin hormone 1

+ +

N

  

5

CSH2

17

Chorionic somatomammotropin hormone 2

+

N

  

6

CGB8

19

Chorionic gonadotropin beta subunit 8

+ +

Almost

Embryonic tissue, skin

 

7

CGB5

19

Chorionic gonadotropin beta subunit 5

+ +

Almost

Embryonic tissue, testis, heart, skin

 

8

SPP1

4

Secreted phosphoprotein 1

N

N

  

9

TMSB10

2

Thymosin beta 10

N

N

  

10

EEF1A1

6

Eukaryotic translation elongation factor 1 alpha 1

N

N

  

11

PEG10

7

Paternally expressed 10

N

N

  

12

FTL

19

Ferritin light chain

N

N

  

13

CGB3

19

Chorionic gonadotropin beta subunit 3

+ +

Almost

Embryonic tissue, connective tissue, testis, ovary

 

14

RPS12

6

Ribosomal protein S12

N

N

  

15

PSG3

19

Pregnancy specific beta-1-glycoprotein 3

+ + +

Almost

Vascular, testis, muscle, kidney, intestine, skin

Term

16

ACTB

7

Actin beta

N

N

  

17

IFI6

1

Interferon alpha inducible protein 6

N

N

  

18

COL3A1

2

Collagen type III alpha 1 chain

N

N

  

19

GDF15

19

Growth differentiation factor 15

+ +

N

 

Term

20

PAGE4

X

PAGE family member 4

+

N

Prostate, heart

 

21

RPS27

1

Ribosomal protein S27

N

N

  

22

ACTG1

17

Actin gamma 1

N

N

  

23

FN1

2

Fibronectin 1

N

N

  

24

RPL13A

19

Ribosomal protein L13a

N

N

  

25

HIST1H1C

6

Histone cluster 1 H1 family member c

N

N

  

26

RPS11

19

Ribosomal protein S11

N

N

  

27

S100A11

1

S100 calcium binding protein A11

N

N

  

28

HIST1H2BK

6

Histone cluster 1 H2B family member k

N

N

  

29

HIST1H3B

6

Histone cluster 1 H3 family member b

No value

Almost

Thymus, liver, kidney, testis

 

30

HIST1H1E

6

Histone cluster 1 H1 family member e

No value

Almost

Mouth, kidney, brain

 

31

PSAP

10

Prosaposin

N

N

  

32

EEF2

19

Eukaryotic translation elongation factor 2

N

N

  

33

RPS18

6

Ribosomal protein S18

N

N

  

34

RPL10A

6

Ribosomal protein L10a

N

N

  

35

CALR

19

Calreticulin

N

N

  

36

HIST1H1B

6

Histone cluster 1 H1 family member b

No value

Almost

Bladder, intestine, skin

 

37

TGM2

20

Transglutaminase 2

N

N

  

38

RPL7A

9

Ribosomal protein L7a

N

N

  

39

SAT1

X

Spermidine/spermine N1-acetyltransferase 1

N

N

  

40

XAGE3

X

X antigen family member 3

+

Yes

  

41

HIST1H4D

6

Histone cluster 1 H4 family member d

No value

Almost

Adipose tissue, vascular

 

42

HSPA8

11

Heat shock protein family A (Hsp70) member 8

N

N

  

43

PSG4

19

Pregnancy specific beta-1-glycoprotein 4

+ +

N

 

Term

44

GAPDH

12

Glyceraldehyde-3-phosphate dehydrogenase

N

N

  

45

EBI3

19

Epstein-Barr virus induced 3

No value*

N

 

Term

46

RPS4X

X

Ribosomal protein S4, X-linked

N

N

  

47

RPS6

9

Ribosomal protein S6

N

N

  

48

RPS8

1

Ribosomal protein S8

N

N

  

49

EFEMP1

2

EGF containing fibulin-like extracellular matrix protein 1

N

N

  

50

RPLP0

12

Ribosomal protein lateral stalk subunit P0

N

N

  

51

ADAM12

10

ADAM metallopeptidase domain 12

+ +

N

 

Term

52

S100A9

1

S100 calcium binding protein A9

N

N

 

Term

53

CYP19A1

15

Cytochrome P450 family 19 subfamily A member 1

+ + +

N

 

Term

54

COL4A1

13

Collagen type IV alpha 1 chain

N

N

  

55

ANXA5

4

Annexin A5

N

N

  

56

RPL19

17

Ribosomal protein L19

N

N

  

57

KRT18

12

Keratin 18

N

N

  

58

XAGE2

X

X antigen family member 2

+ +

Almost

Heart, uterus

 

59

HSP90AB1

6

Heat shock protein 90 alpha family class B member 1

N

N

  

60

HIST1H4C

6

Histone cluster 1 H4 family member c

No value

N

  

61

IGF2

11

Insulin-like growth factor 2

N

N

  

62

HSD3B1

1

Hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1

+ +

N

  

63

EZR

6

Ezrin

N

N

  

64

SLC2A1

1

Solute carrier family 2 member 1

N

N

 

Term

65

RPS2

16

Ribosomal protein S2

N

N

  

66

FBLN1

22

Fibulin 1

+

N

 

Term

67

S100P

4

S100 calcium binding protein P

N

N

 

Term

68

SDC1

2

Syndecan 1

N

N

 

Term

69

HIST1H3F

6

Histone cluster 1 H3 family member f

No value

Almost

Liver, connective tissue, skin

 

70

CTSL

9

Cathepsin L

N

N

  

71

HIST1H4F

6

Histone cluster 1 H4 family member f

No value

Almost

Blood, connective tissue

 

72

PSG1

19

Pregnancy specific beta-1-glycoprotein 1

+ + +

N

 

Term

73

RPS25

11

Ribosomal protein S25

N

N

  

74

PSG5

19

Pregnancy specific beta-1-glycoprotein 5

+ +

N

  

75

PLAC4

21

Placenta specific 4

+ + +

N

  

76

RPL11

1

Ribosomal protein L11

N

N

  

77

SPARC

5

Secreted protein acidic and cysteine rich

N

N

  

78

KRT19

17

Keratin 19

N

N

  

79

PSG2

19

Pregnancy specific beta-1-glycoprotein 2

+ + +

N

  

80

RPL8

8

Ribosomal protein L8

N

N

  

81

HSP90B1

12

Heat shock protein 90 beta family member 1

N

N

  

82

GPC3

X

Glypican 3

N

N

  

83

RPL7

8

Ribosomal protein L7

N

N

  

84

PAPPA2

1

Pappalysin 2

+ +

N

 

Term

85

KRT8

12

Keratin 8

+

N

  

86

RPL5

1

Ribosomal protein L5

N

N

  

87

GH2

17

Growth hormone 2

+

N

  

88

MEST

7

Mesoderm specific transcript

N

N

  

89

RPN2

20

Ribophorin II

N

N

  

90

PRDX5

11

Peroxiredoxin 5

N

N

  

91

GSTP1

11

Glutathione S-transferase pi 1

N

N

  

92

LDHB

12

Lactate dehydrogenase B

N

N

  

93

HIST1H3C

6

Histone cluster 1 H3 family member c

No value

Almost

Testis

 

94

VGLL1

X

Vestigial-like family member 1

+ +

N

  

95

RPL4

15

Ribosomal protein L4

N

N

  

96

ENO1

1

Enolase 1

N

N

 

First

97

PAPPA

9

Pappalysin 1

+ +

N

 

Term

98

COL4A2

13

Collagen type IV alpha 2 chain

N

N

  

99

RPS3A

4

Ribosomal protein S3A

N

N

  

100

SLC40A1

2

Solute carrier family 40 member 1

N

N

  

101

TIMP3

22

TIMP metallopeptidase inhibitor 3

N

N

  

102

ANXA1

9

Annexin A1

N

N

  

103

RPL35

9

Ribosomal protein L35

N

N

  

104

TPT1

13

Tumor protein, translationally controlled 1

N

N

  

105

EPAS1

2

Endothelial PAS domain protein 1

N

N

  

106

HIST1H2BI

6

Histone cluster 1 H2B family member i

No value

Yes

No value in any UniGene body site

 

107

S100A6

1

S100 calcium binding protein A6

N

N

  

108

RPL3

22

Ribosomal protein L3

N

N

  

109

RPL12

9

Ribosomal protein L12

N

N

  

110

DUSP9

X

Dual specificity phosphatase 9

N

N

  

111

PSG9

19

Pregnancy specific beta-1-lycoprotein 9

+ + +

Almost

Vascular, spleen, eye,mammary gland, lung, skin

Term

112

FOXO4

X

Forkhead box O4

+ +

N

  

113

PEG3

19

Paternally expressed 3

N

N

  

114

RPL41

12

Ribosomal protein L41

N

N

  

115

FAM129B

9

Family with sequence similarity 129 member B

N

N

  

116

PDIA3

15

Protein disulfide isomerase family A member 3

N

N

  

117

HIST1H4B

6

Histone cluster 1 H4 family member b

No value

Almost

Lymph node, testis, liver

 

118

MYL12B

18

Myosin light chain 12B

N

N

  

119

HIST1H1D

6

Histone cluster 1 H1 family member d

No value

N

  

120

SPINT1

15

Serine peptidase inhibitor, Kunitz type 1

+

N

  

121

RPLP2

11

Ribosomal protein lateral stalk subunit P2

N

N

  

122

FBN2

5

Fibrillin 2

+

N

  

123

RPS27A

2

Ribosomal protein S27a

N

N

  

124

BSG

19

Basigin (Ok blood group)

N

N

  

125

CTNNB1

3

Catenin beta 1

N

N

  

126

RPL21

13

Ribosomal protein L21

N

N

  

127

COL6A2

21

Collagen type VI alpha 2 chain

N

N

 

First

128

RASA1

5

RAS p21 protein activator 1

+ +

N

  

129

ATP5B

12

ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide

N

N

  

130

RPS20

8

Ribosomal protein S20

N

N

  

131

RPS13

11

Ribosomal protein S13

N

N

  

132

CANX

5

Calnexin

N

N

  

133

ISM2

14

Isthmin 2

+ + +

N

  

134

RPL9

4

Ribosomal protein L9

N

N

  

135

HBG2

11

Hemoglobin subunit gamma 2

N

N

  

136

RACK1

5

Receptor for activated C kinase 1

N

N

  

137

LUM

12

Lumican

N

N

  

138

NPM1

5

Nucleophosmin

N

N

  

139

HIST1H2BO

6

Histone cluster 1 H2B family member o

No value*

Almost

Liver

 

140

PEBP1

12

Phosphatidylethanolamine binding protein 1

N

N

  

141

RPL10

X

Ribosomal protein L10

N

N

  

142

P4HB

17

Prolyl 4-hydroxylase subunit beta

N

N

  

143

IGFBP3

7

Insulin-like growth factor binding protein 3

N

N

  

144

EIF4G2

11

Eukaryotic translation initiation factor 4 gamma 2

N

N

  

145

CD63

12

CD63 molecule

N

N

  

146

PRDX1

1

Peroxiredoxin 1

N

N

  

147

CD24

6

CD24 molecule

N

N

 

First

148

YBX1

1

Y-box binding protein 1

N

N

  

149

BEX3

X

Brain expressed X-linked 3

N

N

  

150

HSPA5

9

Heat shock protein family A (Hsp70) member 5

N

N

  

151

UBC

12

Ubiquitin C

N

N

  

152

MBNL3

X

Muscleblind-like splicing regulator 3

+

N

  

153

RPS19

19

Ribosomal protein S19

N

N

  

154

RPS14

5

Ribosomal protein S14

N

N

  

155

PFN1

17

Profilin 1

N

N

  

156

RHOA

3

Ras homolog family member A

N

N

  

157

HIST1H2BD

6

Histone cluster 1 H2B family member d

N

N

  

158

COX8A

11

Cytochrome c oxidase subunit 8A

N

N

  

159

TCEAL9

X

Transcription elongation factor A like 9

N

N

  

160

TMSB4X

X

Thymosin beta 4, X-linked

N

N

  

161

HSPB8

12

Heat shock protein family B (small) member 8

+

N

 

Term

162

KRT7

12

Keratin 7

N

N

 

First

163

TINAGL1

1

Tubulointerstitial nephritis antigen-like 1

+

N

  

164

RPL27

17

Ribosomal protein L27

N

N

  

165

HSP90AA1

14

Heat shock protein 90 alpha family class A member 1

N

N

  

166

HBA2

16

Hemoglobin subunit alpha 2

N

   

167

RRBP1

20

Ribosome binding protein 1

N

   

168

HMGA1

6

High mobility group AT-hook 1

N

N

 

First

169

TPI1

12

Triosephosphate isomerase 1

N

N

  

170

PTMA

2

Prothymosin, alpha

N

N

  

171

RPSA

3

Ribosomal protein SA

N

N

  

172

CHCHD2

7

Coiled-coil-helix-coiled-coil-helix domain containing 2

N

N

  

173

RPL6

12

Ribosomal protein L6

N

N

  

174

PSG6

19

Pregnancy specific beta-1-glycoprotein 6

+ +

Almost

Vascular, heart, skin, intestine

Term

175

UBB

17

Ubiquitin B

N

N

  
  1. aPlacenta enrichment: (+) = placenta had the highest TPM of any body site on UniGene; (++) = placenta TPM value was one order of magnitude higher than the next-highest body site; (+++) = placenta TPM value was two orders of magnitude higher; N = placenta is not highest; No value = means placenta TPM = 0 on UniGene. *Validation with GSE73016 found expression in term placenta [38]
  2. bPlacenta specificity: “specific” was strictly defined as no expression (TPM = 0) in other healthy body sites on UniGene. “Almost” specific was defined as TPM > 0 in six healthy body sites or less (listed). “N” means gene is expressed in at least seven other tissues (not listed)
  3. cDEGs between early first trimester (“First”, 45–59 days) and term ("Term") placenta based on microarray studies in Mikheev et al. [44]