Table 2.
Gene ontology enrichment analysis highlights distinct biological processes affected by in utero OVA exposure in developing lungs of atopic Brown Norway and normoresponsive Lewis rat
| Gene Ontology Groups Highlighted In In Utero OVA vs. SAL-exposed Rat | No. of Genes in Group | Human Genes | Fold Enrichment | |
|---|---|---|---|---|
| Brown Norway Rat | ||||
| Lipid metabolism | α-1-Acid glycoprotein | 2 | ORM1, ORM2 | 43.50 |
| Phospholipid dephosphorylation | 3 | PPAP2A, PTEN, PP3R1 | 20.75 | |
| Oxidative stress | Age-dependent oxidative stress | 2 | CLN8, SOD2 | 41.50 |
| Intramolecular oxidoreductase | 3 | PDIA4, PTGIS, GREM1 | 11.61 | |
| Nitric oxide mediated signal transduction | 3 | RASD1, DDAH1, APOE | 8.89 | |
| Response to hydrogen peroxide | 7 | HMOX1, TXNIP, GLRX2, SOD2, PRDX3, SDC1, CASP6 | 5.18 | |
| Immune regulation and function | Macrophage chemotaxis | 3 | EDNRB, SFTPD, CKLF | 13.83 |
| Regulation of leukocyte chemotaxis | 3 | CXCL12, IL6R, GREM1 | 11.32 | |
| Positive regulation of phagocytosis | 3 | CALR, SFTPD, MFGE8 | 10.37 | |
| Regulation of phagocytosis | 4 | CALR, PTEN, SFTPD, MFGE8 | 10.37 | |
| Metalloproteinase | 4 | ACE, ADAM15, MMP12, MME | 7.74 | |
| Acute phase | 4 | IL6R, ORM1, ORM2, CFB | 6.41 | |
| Acute inflammatory response | 10 | EPHX2, IL6R, C5, ORM1, C1QC, PTGER3, ORM2, CASP6, KLKB1, CFB | 4.34 | |
| Cell death | Caspases | 3 | CASP7, CFLAR, CASP6 | 10.18 |
| hsa04210:Apoptosis | 8 | MYD88, CYCS, CASP7, CFLAR, BIRC2, CASP6, PPP3CA, PPP3R1 | 3.00 | |
| Negative regulation of apoptosis | 24 | EDNRB, PTEN, BCL2A1, CLN8, SOD2, SOX4, TAX1BP1, ILK, CD74 | 2.98 | |
| Aging | 7 | CALR, SOCS2, CLN8, PTEN, SOD2, ILK, TIMP3 | 2.71 | |
| Regulation of cell death | 44 | CLN8, GCH1, RTEL1, BLOC1S2, PCSK6, IL6R, ACTN4, JAK2, CASP6 | 2.37 | |
| Cell death | 37 | CLN8, GLRX2, CASP6, CASP7, ECE1, RTEL1, ITPR1, PTGER3, HMOX1, DBC1 | 2.24 | |
| Cell proliferation | Regulation of cell growth | 10 | TAF9B, SOCS2, CYR61, CTH, SPHK1, ILK, GREM1, HTRA3, SEMA4F | 2.30 |
| Regulation of cell proliferation | 37 | EDNRB, SFTPD, SOX4, VCAM1, ADAMTS1, MMP12, CD47, COMT, GAL | 2.07 | |
| Positive regulation of cell proliferation | 17 | CCND1, CALR, IL6R, AGGF1, NBN, SOX4, MMP12, CD47, ILK, FIGF, | 1.78 | |
| Negative regulation of cell proliferation | 18 | TOB1, FRK, PTEN, SOD2, BTG2, SFTPD, ADAMTS1, ILK, COMT, GPC3 | 2.12 | |
| Lewis Rat | ||||
| Lipid metabolism | 3-Hydroxyacyl-CoA dehydrogenase | 3 | CRYL1, HADH, HADHA | 18.84 |
| Inositol polyphosphate kinase | 4 | ITPKA, IPMK, IP6K1, ITPKC | 14.36 | |
| Fatty acid elongation in mitochondria | 4 | HADH, MECR, HADHA, PPT2 | 9.74 | |
| Inositol metabolic process | 5 | ITPKA, PTEN, IPMK, SLC5A3 | 5.99 | |
| Angiogenesis/angiotensin | Regulation of angiotensin metabolic process | 3 | ECE1, ACE, ATP6AP2 | 13.48 |
| Cell cycle | Positive regulation of angiogenesis | 6 | RUNX1, BTG1, NOS3, GATA2, ANGPTL4, SPHK1 | 5.18 |
| Microtubules | Cyclins_&_p27_cell cycle | 3 | CDK4, CDKN1B, CDC2 | 11.93 |
| cell cycle control | 6 | CDC25B, CCNA2, MKI67, RBL2, CDK4, CDC2 | 5.16 | |
| DNA replication | 13 | ORC6L, MCM3, GINS4, POLD1, POLD2, RRM2, RFC3, RFC2, DSCC1, LIG1, NASP, RPA2, CHAF1B | 3.94 | |
| Mitosis | 26 | CETN3, CDC2, FAM33A, SETD8, CEP55, PLK1, CDCA3, BUB1B, ACTB, HAUS4, CDCA8, CCNA2, KIFC1, RUVBL1, CENPE, RAN, NCAPD2, SPC25, CDC25B, ARHGEF2, CCNB2, KIF2C, NUF2, TIMELESS, NDE1, CDC20 | 3.79 | |
| Positive regulation of cell cycle | 8 | CALR, TGFA, ID2, SPHK1, EGF, CENPE, PEBP1, ESPL1 | 3.15 | |
| β-Tubulin, autoregulation binding site | 4 | TUBB2C, KIFC2, TUBB6, TUBB | 5.58 | |
| Kinetochore | 11 | SPC25, FAM33A, CENPT, KIF2C, NUF2, NDE1, PLK1, BUB1B, CENPE, NUP107, NUP85 | 4.66 | |
| Microtubule binding | 10 | FAM33A, UXT, ARHGEF2, NDE1, CDK5RAP2, GABARAPL2, KLC3, SBDS, RAE1, TRIM54 | 3.29 | |
| Spindle | 20 | CDCA8, KIF15, SNCG, TUBG1, KIFC1, KIF22, KIF4A, CENPE, SBDS, NUP85, AURKA, CDC2, FAM33A, ARHGEF2, NDE1, PLK1, CDC20, BUB1B, HAUS4, ROCK2 | 3.17 | |
| Microtubule organizing center | 28 | CETN3, ESPL1, AURKA, CEP55, TACC1, PLK1, BUB1B, HAUS4, ROCK2, RAB3IP, MCM3, TSGA14, UXT, KIF15, SNCG, TUBG1, CDK5RAP2, KIFC1, NCRNA00153, RUVBL1, FAM125A, EZR, CDC25B, NME1, NME2, NDE1, NDRG2, ARL2, NDN | 2.58 | |
Not all genes in larger ontology groups are listed. Fold enrichment represents odds ratio that the difference in developmental pattern of expression for genes in the ontology group are a consequence of in utero ovalbumin (OVA) exposure. SAL, saline.