Table 2.
Top DEGs from microarray expression analysis of DA neurons.
| Gene Symbol | Entrez ID | Log FC | adj p val | Description | miRNA target |
|---|---|---|---|---|---|
| (a) Perinatal alcohol exposure | |||||
| Upregulated | |||||
| Lypla2 | 83510 | 9.153 | 1.07E−05 | lysophospholipase 2 |
rno-miR-125a-5p rno-miR-125b-5p rno-miR-434-3p rno-miR-6332 |
| Tprg1l | 687090 | 9.986 | 1.07E−05 | tumor protein p63 regulated 1 like | |
| LOC103689999 | 103689999 | 9.070 | 1.07E−05 | saccharopine dehydrogenase-like oxidoreductase | |
| LOC103690032 | 103690032 | 9.856 | 1.07E−05 | insulinoma-associated protein 1-like | |
| Gnai2 | 81664 | 7.971 | 1.07E−05 | G protein subunit alpha i2 |
rno-miR-129-1-3p rno-miR-129-2-3p rno-miR-30b-5p rno-miR-30d-5p |
| Psmc5 | 81827 | 7.531 | 1.07E−05 | proteasome 26S subunit, ATPase 5 | |
| Ano10 | 301111 | 7.514 | 1.07E−05 | anoctamin 10 | |
| Uba1 | 314432 | 6.827 | 1.15E−05 | ubiquitin-like modifier activating enzyme 1 | |
| Bnip3l | 140923 | 7.468 | 1.17E−05 | BCL2 interacting protein 3 like |
rno-miR-106b-5p rno-miR-20a-5p rno-miR-23b-3p rno-miR-27a-3p rno-miR-27b-3p rno-miR-384-5p rno-miR-129-1-3p rno-miR-129-2-3p rno-miR-30b-5p rno-miR-30d-5p |
| Rpl4 | 64302 | 6.871 | 1.21E−05 | ribosomal protein L4 | |
| Atp5i | 140608 | 7.906 | 1.23E−05 | ATP synthase membrane subunit e | rno-miR-324-3p |
| Derl1 | 362912 | 6.542 | 1.23E−05 | derlin 1 | rno-miR-466b-2-3p |
| Cpsf7 | 365407 | 7.130 | 1.23E−05 | cleavage and polyadenylation specific factor 7 | rno-miR-711 |
| LOC498154 | 498154 | 8.000 | 1.23E−05 | hypothetical protein LOC498154 | |
| Cotl1 | 361422 | 6.275 | 1.23E−05 | coactosin-like F-actin binding protein 1 |
rno-miR-135a-5p rno-miR-30b-5p rno-miR-30d-5p rno-miR-760-3p |
| Atp9a | 84011 | 6.550 | 1.23E−05 | ATPase phospholipid transporting 9A | |
| Atp5g1 | 29754 | 6.185 | 1.23E−05 | ATP synthase membrane subunit c locus 1 |
rno-miR-214-3p rno-miR-3065-3p |
| Cdc37 | 114562 | 7.369 | 1.24E−05 | cell division cycle 37 | |
| Downregulated | |||||
| RGD1564541 | 313433 | − 6.140 | 1.41E−05 | hypothetical protein FLJ22965 |
rno-miR-106b-5p rno-miR-17-5p rno-miR-20a-5p rno-miR-20b-5p |
| Coprs | 290925 | − 7.360 | 1.77E−05 | coordinator of PRMT5 and differentiation stimulator | rno-miR-340-5p |
| LOC102546787 | 102546787 | − 5.790 | 3.63E−05 | uncharacterized LOC102546787 | |
| LOC102552625 | 102552625 | − 6.179 | 4.66E−05 | uncharacterized LOC102552625 | |
| LOC103693454 | 103693454 | − 7.092 | 5.37E−05 | uncharacterized LOC103693454 | |
| Hint2 | 313491 | − 4.330 | 6.76E−05 | histidine triad nucleotide binding protein 2 | |
| Rab33b | 365793 | − 4.538 | 6.76E−05 | member RAS oncogene family | rno-miR-19a-3p |
| LOC102551839 | 102551839 | − 5.450 | 7.27E−05 | uncharacterized LOC102551839 | |
| Got2 | 25721 | − 4.102 | 8.36E−05 | glutamic-oxaloacetic transaminase 2 | rno-miR-384-5p |
| Vav2 | 296603 | − 3.635 | 8.89E−05 | vav guanine nucleotide exchange factor 2 |
rno-miR-15b-5p rno-miR-16-5p rno-miR-195-5p rno-miR-19a-3p rno-miR-27a-3p rno-miR-27b-3p rno-miR-29a-3p rno-miR-322-5p rno-miR-497-5p |
| LOC103690624 | 103690624 | − 5.005 | 9.58E−05 | uncharacterized LOC103690624 | |
| (b) Perinatal nicotine–alcohol exposure | |||||
| Upregulated | |||||
| Lypla2 | 83510 | 9.585 | 6.92E−06 | lysophospholipase 2 |
rno-miR-125a-5p rno-miR-125b-5p rno-miR-434-3p rno-miR-6332 |
| LOC103689999 | 103689999 | 9.378 | 7.03E−06 | saccharopine dehydrogenase-like oxidoreductase | |
| Tprg1l | 687090 | 9.872 | 7.03E−06 | tumor protein p63 regulated 1 like | |
| Psmc5 | 81827 | 7.906 | 7.03E−06 | proteasome 26S subunit, ATPase 5 | |
| Ssbp4 | 364534 | 7.510 | 7.03E−06 | single stranded DNA binding protein 4 | rno-miR-26a-5p |
| LOC103690032 | 103690032 | 9.960 | 7.03E−06 | uncharacterized LOC103690032 | |
| Gnai2 | 81664 | 7.999 | 7.57E−06 | G protein subunit alpha i2 |
rno-miR-129-1-3p rno-miR-129-2-3p rno-miR-30b-5p rno-miR-30d-5p |
| Atp9a | 84011 | 7.417 | 7.62E−06 | ATPase phospholipid transporting 9A | |
| Uba1 | 314432 | 7.100 | 7.62E−06 | ubiquitin-like modifier activating enzyme 1 | |
| Ano10 | 301111 | 7.457 | 7.62E−06 | anoctamin 10 | |
| Atp5g1 | 29754 | 6.851 | 7.62E−06 | ATP synthase membrane subunit c locus 1 |
rno-miR-214-3p rno-miR-3065-3p |
| Bnip3l | 140923 | 7.773 | 8.15E−06 | BCL2 interacting protein 3 like |
rno-miR-129-1-3p rno-miR-129-2-3p rno-miR-137-3p rno-miR-30b-5p rno-miR-30d-5p rno-miR-20a-5p rno-miR-23b-3p rno-miR-27a-3p rno-miR-27b-3p rno-miR-384-5p rno-miR-26a-5p |
| Derl1 | 362912 | 6.952 | 8.45E−06 | derlin 1 |
rno-miR-466b-2-3p rno-miR-26a-5p |
| Sema4a | 310630 | 7.562 | 8.48E−06 | semaphorin 4A | |
| Npdc1 | 296562 | 6.914 | 9.31E−06 | neural proliferation, differentiation and control, 1 | rno-miR-760-3p |
| LOC498154 | 498154 | 8.113 | 9.31E−06 | hypothetical protein LOC498154 | rno-let-7e-5p |
| Vamp3 | 29528 | 7.066 | 9.31E−06 | vesicle-associated membrane protein 3 | rno-miR-34c-5p |
| Cdc37 | 114562 | 7.642 | 9.31E−06 | cell division cycle 37 | rno-miR-99b-5p |
| Atp5i | 140608 | 7.934 | 9.31E−06 | ATP synthase membrane subunit e | rno-miR-324-3p |
| LOC102546798 | 102546798 | 9.532 | 9.31E−06 | uncharacterized LOC102546798 | |
| Downregulated | |||||
| RGD1564541 | 313433 | − 6.121 | 1.10E−05 | similar to hypothetical protein FLJ22965 |
rno-miR-20a-5p rno-miR-20b-5p rno-miR-17-5p |
| Coprs | 290925 | − 7.780 | 1.26E−05 | coordinator of PRMT5 and differentiation stimulator | rno-miR-340-5p |
| Hint2 | 313491 | − 4.669 | 4.28E−05 | histidine triad nucleotide binding protein 2 | |
| LOC102546787 | 102546787 | − 5.142 | 5.94E−05 | uncharacterized LOC102546787 | |
| Rab33b | 365793 | − 4.539 | 6.32E−05 | member RAS oncogene family | rno-miR-19a-3p |
| Snrpd3 | 687711 | − 4.206 | 7.25E−05 | small nuclear ribonucleoprotein D3 polypeptide | |
| Ufd1l | 84478 | − 5.237 | 7.64E−05 | ubiquitin recognition factor in ER associated degradation 1 | |
| LOC102551839 | 102551839 | − 5.315 | 7.82E−05 | uncharacterized LOC102551839 | |
| Cr1l | 54243 | − 5.646 | 8.74E−05 | complement C3b/C4b receptor 1 like | rno-miR-15b-5p |
| (c) Perinatal nicotine–alcohol exposure vs. alcohol exposure | |||||
| Upregulated | |||||
| Gnl3 | 290,556 | 3.598 | 5.13E−05 | guanine nucleotide binding protein-like 3 (nucleolar) | |
| Usp34 | 360,990 | 3.908 | 5.60E−05 | ubiquitin specific peptidase 34 | |
| Fam91a1 | 689,997 | 3.925 | 9.43E−05 | family with sequence similarity 91 | |
| Bbs5 | 362,142 | 3.507 | 9.57E−05 | Bardet-Biedl syndrome 5 | |
| RGD1566401 | 500,717 | 3.991 | 9.66E−05 | similar to GTL2 | |
| Rars | 287,191 | 3.882 | 1.25E−04 | arginyl-tRNA synthetase | |
| Hmbox1 | 305,968 | 3.757 | 1.25E−04 | homeobox containing 1 |
rno-miR-137-3p rno-miR-34c-5p rno-miR-34b-5p |
| Kidins220 | 116,478 | 3.949 | 1.32E−04 | kinase D-interacting substrate 220 |
rno-miR-34c-5p rno-miR-34b-5p |
| Ptbp2 | 310,820 | 3.703 | 1.38E−04 | polypyrimidine tract binding protein 2 | |
| Tubg2 | 680,991 | 3.542 | 1.51E−04 | tubulin | |
| Ccdc50 | 288,022 | 3.577 | 1.52E−04 | coiled-coil domain containing 50 | rno-miR-137-3p |
| Impdh1 | 362,329 | 3.475 | 1.54E−04 | IMP (inosine 5′-monophosphate) dehydrogenase 1 | rno-miR-100-5p |
| Ppwd1 | 294,711 | 4.105 | 1.63E−04 | peptidylprolyl isomerase domain and WD repeat containing 1 | |
| Rdx | 315,655 | 3.776 | 1.78E−04 | radixin |
rno-let-7a-5p rno-let-7f.-5p |
| Rapgef2 | 310,533 | 3.749 | 1.85E−04 | Rap guanine nucleotide exchange factor (GEF) 2 | |
| RGD1566401 | 500,717 | 4.177 | 1.89E−04 | similar to GTL2 | |
| Cacna1b | 257,648 | 3.542 | 1.98E−04 | calcium channel | |
| Cst3 | 25,307 | 3.970 | 1.99E−04 | cystatin C | |
| Ubxn2b | 312,965 | 3.712 | 2.16E−04 | UBX domain protein 2B | |
| Slc7a3 | 29,485 | 3.661 | 2.23E−04 | solute carrier family 7 (cationic amino acid transporter | |
| Cdc42 | 64,465 | 3.715 | 2.83E−04 | cell division cycle 42 | rno-miR-137-3p |
| Downregulated | |||||
| Zc2hc1b | 100,361,672 | − 5.757 | 5.60E−05 | zinc finger | |
| Zc3hav1 | 252,832 | − 5.510 | 5.60E−05 | zinc finger CCCH type | |
| Ptms | 83,801 | − 4.221 | 5.60E−05 | parathymosin | |
| Hmx1 | 360,960 | − 3.841 | 6.64E−05 | H6 family homeobox 1 | |
| Etv3 | 295,297 | − 5.703 | 7.57E−05 | ets variant 3 | |
| Kmt2d | 100,362,634 | − 3.476 | 7.57E−05 | lysine (K)-specific methyltransferase 2D | |
| Gimap8 | 500,112 | − 5.896 | 7.97E−05 | GTPase | |
| Sfpq | 252,855 | − 3.246 | 9.59E−05 | splicing factor proline/glutamine-rich | |
| Cass4 | 296,409 | − 3.950 | 9.66E−05 | Cas scaffolding protein family member 4 | |
| Elac1 | 307,604 | − 3.324 | 9.66E−05 | elaC ribonuclease Z 1 | |
| Pamr1 | 311,252 | − 3.305 | 9.66E−05 | peptidase domain containing associated with muscle regeneration 1 | |
| Kcnj9 | 116,560 | − 3.897 | 1.01E−04 | potassium channel | |
| Rmrp | 29,536 | − 3.885 | 1.25E−04 | RNA component of mitochondrial RNA processing endoribonuclease | |
| Ift57 | 303,968 | − 5.138 | 1.25E−04 | intraflagellar transport 57 | |
| Hes7 | 287,423 | − 4.184 | 1.27E−04 | hes family bHLH transcription factor 7 | |
| Ubxn1 | 293,719 | − 3.527 | 1.54E−04 | UBX domain protein 1 | |
| Araf | 64,363 | − 3.510 | 1.73E−04 | A-Raf proto-oncogene | |
| Foxe1 | 192,274 | − 5.828 | 1.76E−04 | forkhead box E1 | |
| Lzts3 | 280,670 | − 3.317 | 1.77E−04 | leucine zipper | |
| Ccnf | 117,524 | − 3.384 | 1.78E−04 | cyclin F | |
| Hs3st3b1 | 303,218 | − 4.901 | 1.85E−04 | heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1 | |
| Aig1 | 292,486 | − 3.523 | 1.85E−04 | androgen-induced 1 | |
| Bcl11a | 305,589 | − 4.236 | 1.92E−04 | B-cell CLL/lymphoma 11A (zinc finger protein) | |
| Tbx21 | 303,496 | − 3.445 | 2.03E−04 | T-box 21 | |
| Avil | 79,253 | − 3.577 | 2.11E−04 | advillin | |
| Plcb2 | 85,240 | − 3.427 | 2.17E−04 | phospholipase C | |
| RatNP-3b | 498,659 | − 4.205 | 2.21E−04 | defensin RatNP-3 precursor | |
| Srcap | 361,652 | − 3.261 | 2.23E−04 | Snf2-related CREBBP activator protein | |
| Lmnb1 | 116,685 | − 3.286 | 2.24E−04 | lamin B1 | |
| Elf2 | 361,944 | − 4.757 | 2.25E−04 | E74-like factor 2 | rno-miR-29b-3p |
| Phtf1 | 252,962 | − 5.586 | 2.34E−04 | putative homeodomain transcription factor 1 | |
| Mospd2 | 363,463 | − 3.669 | 2.39E−04 | motile sperm domain containing 2 | rno-miR-29b-3p |
(a) List of most significant up and downregulated DEGs following perinatal alcohol exposure compared to saline control. (b) List of most significant up and downregulated DEGs following perinatal nicotine-alcohol exposure compared to saline control. (c) List of most significant up and downregulated DEGs following perinatal nicotine-alcohol exposure compared to alcohol exposure. The genes were listed after Benjamini–Hochberg corrections with adjusted p value < 0.001, q value < 0.05 and absolute log2 fold change > 1. Predicted miRNA targets were also included in both lists.