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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

From: Effects of sustained hyperprolactinemia in late gestation on the mammary parenchymal tissue transcriptome of 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

  1. 1Count = number of genes
  2. 2Bold = up-regulated genes and Plain text = down-regulated genes in T20 compared with CTL gilts; Underlined = genes that were validated with qPCR analysis
  3. 3FES = Fold Enrichment Score
  4. 4Gene ontology term enrichment P-values; †, tendency after Benjamini-Hochberg correction