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)