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Table 3 Enriched functions of DE genes in the Down and Up group using DAVID (89% grain vs. 72% grain)

From: Transcriptome analysis of ruminal epithelia revealed potential regulatory mechanisms involved in host adaptation to gradual high fermentable dietary transition in beef cattle

GO terms P value Molecules
Down Group
Down-regulated genes (n = 45)
 GO:0045087~innate immune response 8.2E-05 EIF2AK2, MX1, S100A9, C2, NLRC5, C1QB
 GO:0042742~defense response to bacterium 1.2E-04 ISG15, CXCL5, TAP
 GO:0006958~complement activation, classical pathway 2.7E-04 C3, C2, C1QB
 GO:0051607~defense response to virus 9.8E-04 OAS1Y, ISG15, MX1, NLRC5
 GO:0045071~negative regulation of viral genome replication 1.2E-03 EIF2AK2, ISG15, MX1
 GO:0009636~response to toxic substance 2.4E-03 EIF2QK2, CYP1A1, CYP1B1
 GO:0009404~toxin metabolic process 1.1E-02 CYP1A1, CYP1B1
 GO:2,000,427~positive regulation of apoptotic cell clearance 1.5E-02 C3, C2
 GO:0006956~complement activation 1.8E-02 C3, C2
 GO:0034340~response to type I interferon 2.2E-02 ISG15, MX1
 GO:0006955~immune response 2.2E-02 OAS1Y, CXCL5, LOC504773
 GO:0070098~chemokine-mediated signaling pathway 4.7E-02 CXCL5, LOC504773
Up-regulated genes (n = 22)
 GO:0035914~skeletal muscle cell differentiation 3.2E-02 EGR1, FOS
Up Group
Down-regulated genes (n = 163)
 GO:0051301~cell division 4.4E-09 SKA3, ASPM, CKS2, PTTG1, CCNB1, BIRC5, CCNB2, AURKA, SPC24, NCAPH, UBE2C, CCNA2, CDCA3, SPDL1, TPX2
 GO:0007080~mitotic metaphase plate congression 6.0E-05 KIF22, KIFC1, CDCA8, KIF2C, CCNB1, SPDL1
 GO:0007018~microtubule-based movement 1.1E-04 KIF22, KIFC1, KIF2C, KIF11, KIF20A, CENPE
 GO:0007059~chromosome segregation 3.1E-04 SKA3, SLC25A5, KIF11, CENPT, BIRC5, HJURP
 GO:0007067~mitotic nuclear division 3.8E-04 PLK1, SKA3, ASPM, CCNA2, PTTG1, CCNB2, NUF2, SPC24
 GO:0031577~spindle checkpoint 6.1E-04 AURKB, BIRC5, SPDL1
 GO:0045143~homologous chromosome segregation 6.1E-04 PLK1, ESPL1, PTTG1
 GO:0000070~mitotic sister chromatid segregation 1.4E-03 PLK1, CDCA8, ESPL1, SPAG5
 GO:0051988~regulation of attachment of spindle microtubules to kinetochore 2.0E-03 RACGAP1, ECT2, SPAG5
 GO:0007052~mitotic spindle organization 2.7E-03 AURKB, CCNB1, NDC80, AURKA
 GO:0000281~mitotic cytokinesis 4.1E-03 PLK1, RACGAP1, KIF20A, CKAP2
 GO:0090307~mitotic spindle assembly 5.3E-03 KIFC1, KIF11, BIRC5, TPX2
 GO:0034501~protein localization to kinetochore 5.4E-03 AURKB, SPDL1, BUB1B
 GO:0010628~positive regulation of gene expression 6.7E-03 MAPK11, CAV1, ACTA2, FN1, ACTG2, VIM
 GO:0000910~cytokinesis 8.0E-03 CIT, KIF20A, BIRC5, ECT2
 GO:0007094~mitotic spindle assembly checkpoint 1.2E-02 PLK1, BUB1B, BUB1
 GO:0071346~cellular response to interferon-gamma 1.9E-02 SLC26A6, GAPDH, LOC504773
 GO:0001578~microtubule bundle formation 2.4E-02 PLK1, KIF20A, TPPP3
 GO:0006096~glycolytic process 2.7E-02 GAPDH, ENO1, ENO2
 GO:0035606~peptidyl-cysteine S-trans-nitrosylation 2.8E-02 GAPDH, S100A9
 GO:0006816~calcium ion transport 3.9E-02 CAV1, ANXA6, CACNA1G
 GO:0045931~positive regulation of mitotic cell cycle 3.9E-02 CCNB1, BIRC5, CDC25B
Up-regulated genes (n = 122)
 GO:0043507~positive regulation of JUN kinase activity 1.4E-02 FZD5, EDN1, EPHA4
 GO:2,001,237~negative regulation of extrinsic apoptotic signaling pathway 2.6E-02 PHIP, ITGAV, TGFBR1
 GO:0009404~toxin metabolic process 2.9E-02 CYP1A1, CYP1B1
 GO:0018406~protein C-linked glycosylation via 2′-alpha-mannosyl-L-tryptophan 2.9E-02 DPY19L3, DPY19L4
 GO:0002904~positive regulation of B cell apoptotic process 2.9E-02 FNIP1, CD24
 GO:0042632~cholesterol homeostasis 3.0E-02 CD24, ABCA1, EPHX2
 GO:0017144~drug metabolic process 3.8E-02 CYP1A1, FMO5
 GO:0045944~positive regulation of transcription from RNA polymerase II promoter 4.1E-02 PHIP, TET2, FZD5, EDN1, CCNT1, FOS, NRIP1, MYSM1, PCGF5