Table 2.
Over-represented Gene Ontology (GO) terms within the biological process and molecular function categories using differentially-expressed genes in the mammary parenchyma of T20 vs CTL gilts
| DAVID (version 6.8) | Count1 | Gene Symbols2 | FES3 | P-value4 |
|---|---|---|---|---|
| GOTERM - Biological Process – DIRECT | ||||
| Negative regulation of apoptotic process GO:0043066 | 20 | APBB2, BIRC5, CAT, CITED2, CTSH, DAB2, FOXO1, HSPA5, HSP90AB1, IGF1R, LTF, MYC, NPM1, PIM1, PRNP, PSEN2, RARG, RPS3A, SOX9, STAT3 | 2.5 | 3.5E-4† |
| Metabolic process GO:0008152 | 11 | ACSF2, ACSL3, ACSS3, AGPAT3, ARSA, LCLAT1, MAN1A1, SCP2, SUCLG1, SULF2, UGT8 | 3.4 | 0.0015 |
| Oxidation-reduction process GO:0055114 | 14 | AKR1B1, ALDH2, CAT, CYP4A24, CYP51, DUOX1, ETFB, FMO2, GPX1, HSD17B8, MAOB, PRDX6, SCD, SOD2 | 2.5 | 0.0035 |
| Positive regulation of I-kappaB kinase/NF-kappaB signaling GO:0043123 | 11 | CASP1, CTNNB1, ECM1, LITAF, LTF, MID2, MYD88, NOD1, S100A12, S100B, TRIM13 | 3.0 | 0.0038 |
| Regulation of gene expression GO:0010468 | 8 | DNMT3A, DNMT3B, EIF4A2, FAM46A, MEGF8, PHLDA2, SHC4, TC2N | 3.7 | 0.0051 |
| Innate immune response GO:0045087 | 15 | C3, C9, CD14, CD59, HMGB2, JCHAIN, MID2, MYD88, PGLYRP1, S100A12, TLR2, TLR4, TMEM173, TNK2, TRIM1 | 2.2 | 0.0080 |
| Positive regulation of NF-kappaB transcription factor activity GO:0051092 | 9 | CAT, LTF, MID2, NOD1, NPM1, PRDX3, RIPK3, TLR2, TRIM13 | 3.1 | 0.0082 |
| Apoptotic process GO:0006915 | 9 | BIRC5, CASP1, CIDEA, CTSH, FOXO1, RPS3, SHC4, STK26, TMEM173 | 2.6 | 0.0160 |
| Inflammatory response GO:0006954 | 15 | ACKR2, AIMP1, C3, CCL23, CD14, CXCL2, CXCL8, ECM1, MYD88, ODAM, P2RX7, PTGER4, S100A12, TLR2, TLR4 | 2.0 | 0.0190 |
| Positive regulation of cell proliferation GO:0008284 | 15 | CDCA7L, CTSH, EMP2, FOLR2, MYC, MZB1, NPM1, NTRK3, PDGFC, PRDX3, PTPN6, RARG, SHC4, SOX9, TGFA | 2.0 | 0.0190 |
| Response to lipopolysaccharide GO:0032496 | 8 | CASP1, CXCL2, CXCL8, CYP27B1, HMGB2, P2RX7, PRDX3, PTGER4 | 2.7 | 0.0270 |
| GOTERM - Molecular Function – DIRECT | ||||
| Structural constituent of ribosomes GO: 0003735 | 18 | MRPL14, MRPL46, RPL5, RPL9, RPL10A, RPL11, RPL22, RPL24, RPL27, RPL31, RPL34, RPL35A, RPL36, RPS3, RPS3A, RPS20, SLC25A35, SLC25A36 | 2.3 | 0.0019 |
| Poly(A) RNA binding GO:0003723 | 40 | ALDH6A1, BTF3, C1H14orf166, CDC5L, CSRP1, DSP, EIF3D, EIF3G, EIF4A2, FAM46A, FTSJ3, GRN, HMGN2, HNRNPA1, HSP90AB1, IPO5, KHDRBS1, LSM3, MRPL14, NAF1, NAP1L1, NOP16, NPM1, NSA2, PABPC4, PDIA4, PEBP1, RAVER2, RPL11, RPL22, RPL27, RPL36, RPS20, RPS3A, SNRPD1, SNRPG, SSRP1, SUB1, SUCLG1, TRAP1 | 1.5 | 0.0120 |
| Chromatin DNA binding GO:0031490 | 6 | EZH2, GRHL3, PPARGC1A, STAT3, THRB, WBP2 | 4.1 | 0.0150 |
| RNA binding GO:0003723 | 15 | CIRBP, LSM3, MRPL39, PPARGC1A, RPL9, RPL10A, RPL22, RPL34, RPS3, RPS20, SMN1, SNRPD1, SNRPE, SNRPF, UBR5 | 2.0 | 0.0210 |
| Zinc ion binding GO:0008270 | 43 | ADAMTS6, ADAMTS9, ANPEP, BIRC5, BMP1, CPM, CSRP1, CSRP2, DMD, DTNB, DTX4, KAT7, LIMK2, LTA4H, MAN2A1, MID2, MMP16, MT-2B, MYLIP, NRAP, PAM, PAPLN, PDLIM1, PGLYRP1, PHC1, RARG, RNF113A, RNF125, RNF144B, RUFY1, S100A12, S100B, SEC24A, TET1, THRB, TRAF7, TRIM13, UBR5, VDR, ZCCHC11, ZDHHC2, ZMIZ1, ZNRF3 | 1.3 | 0.0480 |
1Count = number of genes
2Bold = up-regulated genes and Plain text = down-regulated genes in T20 compared with CTL gilts; Underlined = genes that were validated with qPCR analysis
3FES = Fold Enrichment Score
4Gene ontology term enrichment P-values; †, tendency after Benjamini-Hochberg correction