Table 2.
Genes with parent-of-origin driven allelic expression in the human placenta
| 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. |
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
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)
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)
cSources of the previously reported parental allelic expression information are provided in Additional file 4: Table S3
d Data from Geneimprint database (http://www.geneimprint.com/)
FPKM, fragments per kilobase of transcript per million mapped reads; Mat, maternal; Pat, paternal; SD, standard deviation; n.a., not available
eMaternal allelic expression was experimentally confirmed by RT-PCR, cloning, and sequencing (Additional file 10: Table S7)