Table 1.
Overlapping, differentially methylated loci (DMLs) and differentially expressed genes (DEGs).
| Chr | start | end | symbol | Ensembl ID | biotype | Inside Feature | Bm | lg2FC | lfcSE | stat | P-value | P adj |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| (A) | Contrast (GE1): [(Tph2+/- MS-Tph2+/- C)-(Tph2+/+ MS-Tph2+/+ C)] | |||||||||||
| DML | ||||||||||||
| 13 | 36365737 | 36366424 | Fars2 | ENSMUSG00000021420 | protein_coding | inside | 15.46 | -0.74 | 0.21 | -3.57 | 3.64E-04 | 0.96 |
| 13 | 69457460 | 69458618 | Nsun2 | ENSMUSG00000021595 | protein_coding | upstream | 37.21 | -0.52 | 0.19 | -2.79 | 5.34E-03 | 1.00 |
| 9 | 121477914 | 121478574 | Cck | ENSMUSG00000032532 | protein_coding | downstream | 16.13 | 0.58 | 0.21 | 2.81 | 4.98E-03 | 1.00 |
| 1 | 3583857 | 3584649 | Xkr4 | ENSMUSG00000051951 | protein_coding | inside | 17.95 | 0.75 | 0.21 | 3.60 | 3.14E-04 | 0.96 |
| 5 | 90554052 | 90554958 | 5830473C10Rik | ENSMUSG00000070690 | protein_coding | upstream | 24.92 | -0.69 | 0.19 | -3.57 | 3.57E-04 | 0.96 |
| 2 | 98661728 | 98665716 | Gm10801 | ENSMUSG00000075015 | protein_coding | includeFeature | 96234.69 | -0.44 | 0.12 | -3.50 | 4.62E-04 | 1.00 |
| 7 | 73774794 | 73775963 | A830073O21Rik | ENSMUSG00000091890 | protein_coding | upstream | 33.84 | 0.47 | 0.18 | 2.61 | 9.12E-03 | 1.00 |
| 10 | 112610921 | 112611527 | Gm26596 | ENSMUSG00000097185 | protein_coding | upstream | 15.17 | -0.55 | 0.21 | -2.64 | 8.40E-03 | 1.00 |
| DEG | ||||||||||||
| 13 | 36117411 | 36537592 | Fars2 | ENSMUSG00000021420 | protein_coding | 10.02 | -0.99 | 0.28 | -3.59 | 3.37E-04 | 0.08 | |
| 13 | 69533746 | 69635780 | Nsun2 | ENSMUSG00000021595 | protein_coding | 5.67 | -0.84 | 0.26 | -3.18 | 1.45E-03 | 0.14 | |
| 9 | 121489825 | 121495689 | Cck | ENSMUSG00000032532 | protein_coding | 1.96 | -0.74 | 0.27 | -2.74 | 6.10E-03 | NA∗ | |
| 1 | 3205901 | 3671498 | Xkr4 | ENSMUSG00000051951 | protein_coding | 3.54 | -0.74 | 0.29 | -2.59 | 9.62E-03 | NA∗ | |
| 5 | 90561107 | 90597871 | 5830473C10Rik | ENSMUSG00000070690 | protein_coding | 0.47 | 0.51 | 0.17 | 2.94 | 3.23E-03 | NA∗ | |
| 2 | 98662237 | 98664083 | Gm10801 | ENSMUSG00000075015 | protein_coding | 3.17 | -0.86 | 0.26 | -3.34 | 8.38E-04 | NA∗ | |
| 7 | 73737929 | 73741024 | A830073O21Rik | ENSMUSG00000091890 | TEC | 28.22 | -0.64 | 0.24 | -2.63 | 8.47E-03 | 0.35 | |
| 10 | 112928501 | 112931155 | Gm26596 | ENSMUSG00000097185 | protein_coding | 332.56 | -0.48 | 0.19 | -2.59 | 9.58E-03 | 0.37 | |
| (B) | Contrast (GE2): [(Tph-/- MS-Tph2-/- C)-(Tph2+/+ MS-Tph2+/+ C)] | |||||||||||
| DML | ||||||||||||
| 5 | 135031000 | 135031630 | Stx1a | ENSMUSG00000007207 | protein_coding | inside | 18.88 | -0.56 | 0.21 | -2.68 | 7.39E-03 | 1.00 |
| 2 | 35326274 | 35327079 | Stom | ENSMUSG00000026880 | protein_coding | inside | 21.99 | 0.59 | 0.20 | 2.95 | 3.13E-03 | 1.00 |
| 2 | 4594896 | 4595707 | Gm13179 | ENSMUSG00000086018 | antisense | upstream | 16.98 | -0.56 | 0.21 | -2.65 | 8.13E-03 | 1.00 |
| DEG | ||||||||||||
| 5 | 135023482 | 135051100 | Stx1a | ENSMUSG00000007207 | protein_coding | 2.28 | -0.71 | 0.27 | -2.59 | 9.58E-03 | 1.00 | |
| 2 | 35313986 | 35336976 | Stom | ENSMUSG00000026880 | protein_coding | 0.37 | -0.47 | 0.16 | -2.91 | 3.67E-03 | 1.00 | |
| 2 | 4586024 | 4587287 | Gm13179 | ENSMUSG00000086018 | antisense | 58.62 | 0.42 | 0.15 | 2.73 | 6.27E-03 | 1.00 | |
List of genes that had been affected by gene-by-environment interaction of tryptophan hydroxylase 2 (Tph2) genotype and maternal separation (MS), (GE1 [(Tph2+/- MS-Tph2+/- C)-(Tph2+/+ MS-Tph2+/+ C)] and GE2 [(Tph2-/- MS-Tph2-/- C)-(Tph2+/+ MS-Tph2+/+ C)]; reported under A and B, respectively). Data based on sequencing counts of total RNA and methyl-CpG-binding domain (MBD) capture-based, enriched loci (n/group = 6–8). Chr, chromosome; Bm, base mean; lg2FC, log2 fold change; lfcSE, log2 fold change standard error; stat, Wald-statistic; lincRNA, long intergenic non-coding RNA; lncRNA, long non-coding RNA; p adj, adjusted p-value; TEC, to be experimentally confirmed. Fars2, phenylalanine-tRNA synthetase 2 (mitochondrial); Nsun2, NOL1/NOP2/Sun domain family member 2; Cck, cholecystokinin; Xkr4, X-linked Kx blood group related 4; 5830473C10Rik, RIKEN cDNA 5830473C10 gene; Gm10801, predicted gene 10801; A830073O21Rik, RIKEN cDNA A830073O21 gene; Gm26596, predicted gene 26596; Stx1a, syntaxin 1A (brain); Stom, stomatin; Gm13179, predicted gene 13179. ∗Using the default settings of DESeq2; samples with certain criteria like low Bm are excluded from the analysis of p adj. As our analysis was based on nominal p-values; the standard analysis was not adapted.