Skip to main content

Table 2 Genes with parent-of-origin driven allelic expression in the human placenta

From: Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy

Gene

FPKM

Mean (SD)a

RNA-Seq reads

Binominal test corrected P valueb

Locus class

Expressed allele

Imprinting in mouse (expressed allele)d

Mat

Pat

Maternal read proportion (95%CI)

This study

Previous studies c

MEG3

104.0 (83.7)

5002

23

1 (0.99–1)

< 2.2 × 10−300

Imprinted

Mat

Mat

Imprinted (Mat)

PHLDA2

5.9 (4.1)

154

5

0.97 (0.94–0.99)

2.2 × 10−37

Imprinted

Mat

Mat

Imprinted (Mat)

RTL1

4.0 (3.0)

687

35

0.95 (0.94–0.96)

4.3 × 10−156

Imprinted

Mate

Pat

Imprinted (Pat)

H19

498.0 (319.3)

20522

1393

0.94 (0.93–0.94)

4.7 × 10−322

Imprinted

Mat

Mat

Imprinted (Mat)

PEG10

102.1 (49.8)

13

6101

0 (0–0)

<2.2 × 10−300

Imprinted

Pat

Pat

Imprinted (Pat)

IGF2

84.5 (54.8)

52

6695

0.01 (0.01–0.01)

<2.2 × 10−300

Imprinted

Pat

Pat

Imprinted (Pat)

MEST

97.3 (52.3)

10

850

0.01 (0.01–0.02)

1.5 × 10−234

Imprinted

Pat

Pat

Imprinted (Pat)

ZFAT

101.8 (24.0)

138

9652

0.01 (0.01–0.02)

4.7 × 10−322

imprinted

Pat

Pat

Biallelic

PLAGL1

22.7 (9.5)

10

402

0.02 (0.01–0.04)

6.5 × 10−103

Imprinted

Pat

Pat

Imprinted (Pat)

DLK1

54.9 (41.7)

50

1467

0.03 (0.03–0.04)

<2.2 × 10−300

Imprinted

Pat

Pat

Imprinted (Pat)

AIM1

55.6 (17.8)

65

971

0.06 (0.05–0.08)

4.3 × 10−206

Imprinted

Pat

Pat

n.a.

KLHDC10

5.8 (1.4)

248

83

0.75 (0.71–0.79)

3.0 × 10−18

Biased

Mat

Mat

n.a.

NLRP2

14.9 (5.8)

697

282

0.71 (0.69–0.74)

3.3 × 10−39

Biased

Mat

Mat

n.a.

GRB10

9.9 (4.7)

302

146

0.67 (0.64–0.71)

1.3 × 10−11

Biased

Mat

Isoform dependent

Imprinted (isoform dependent)

NAA60

6.0 (1.3)

164

82

0.67 (0.61–0.72)

1.8 × 10−5

Biased

Mat

Mat

n.a.

CPXM2

9.1 (10.79)

72

588

0.11 (0.09–0.13)

1.36 × 10−99

Biased

Pat

Pat

n.a.

MCCC1

4.3 (1.0)

14

101

0.12 (0.08–0.18)

1.9 × 10−15

Biased

Pat

Pat

n.a.

PLEKHG4B

0.9 (0.7)

52

292

0.15 (0.12–0.19)

1.1 × 10−39

Biased

Pat

Pat

n.a.

DCAF10

4.2 (0.7)

15

78

0.16 (0.1–0.24)

1.9 × 10−9

Biased

Pat

Pat

n.a.

DNMT1

8.9 (4.7)

71

353

0.17 (0.14–0.2)

4.5 × 10−44

Biased

Pat

Pat

n.a.

NUDT12

2.1 (0.9)

5

24

0.17 (0.07–0.33)

5 × 10−2

Biased

Pat

Pat

n.a.

RHOBTB3

358.0 (130.8)

2264

10119

0.18 (0.18–0.19)

4.7 × 10−322

Biased

Pat

Pat

n.a.

ZDBF2

8.9 (2.4)

226

878

0.2 (0.18–0.23)

3.7 × 10−89

Biased

Pat

Pat

Imprinted (Pat)

MKRN3

3.5 (1.0)

44

102

0.3 (0.24–0.37)

1.7 × 10−4

Biased

Pat

Pat

Imprinted (Pat)

GRHL1

28.7 (7.0)

1825

3399

0.35 (0.34–0.36)

1.2 × 10−104

Biased

Pat

Pat

n.a.

  1. Results of the binominal test, parental allelic proportions, and expressional information for the full analyzed dataset of 91 genes is provided in Additional file 7: Table S5 and Additional file 8: Table S6
  2. aGene expression level across all analyzed placental samples, including the three trimesters of uncomplicated pregnancy and four clinical subgroups of complicated pregnancies (preeclampsia, gestational diabetes, delivery of a small- or large-for gestational age newborn)
  3. bThe observed parental transcript ratios were statistically tested under the assumption that both alleles are expressed at equal levels, using binomial test implemented in R. Statistical significance level was defined P < 0.05 after application of Bonferroni correction for the number of conducted tests (n = 91)
  4. cSources of the previously reported parental allelic expression information are provided in Additional file 4: Table S3
  5. d Data from Geneimprint database (http://www.geneimprint.com/)
  6. FPKM, fragments per kilobase of transcript per million mapped reads; Mat, maternal; Pat, paternal; SD, standard deviation; n.a., not available
  7. eMaternal allelic expression was experimentally confirmed by RT-PCR, cloning, and sequencing (Additional file 10: Table S7)
Back to article page

Clinical Epigenetics

ISSN: 1868-7083

Contact us