Table 1.
The KEGG pathway enrichment by up−/down-regulated genes in the mammary gland of cows fed corn stover (CS) vs. alfalfa hay (AH)
| KEGG ID | Pathway Name | P-value of Fisher’ exact Test | No. of Increased Genes | ID of Increased Genes | Gene Symbol of Increased Genes | No. of Decreased Genes | ID of Decreased Genes | Gene Symbol of Decreased Genes |
|---|---|---|---|---|---|---|---|---|
| ko04974 | Protein digestion and absorption | 0.0269 | 0 | 7 | XLOC_022008;XLOC_001311; XLOC_000568;XLOC_027248; XLOC_000569;XLOC_017584; XLOC_020771 |
SLC38A2; SLC7A8; BT.23508; COL12A1; COL6A2; COL17A1; COL6A3 | ||
| ko04141 | Protein processing in endoplasmic reticulum | 0.0450 | 10 | XLOC_000859;XLOC_003872;XLOC_006584;XLOC_009297;XLOC_020319;XLOC_022100;XLOC_024455;XLOC_025681;XLOC_026233;XLOC_027001 | HSPH1;DNAJB1;DNAJA1;DDIT3;CRYAB;SAR1B;BT.59327;MAN1A2;SEC63;DNAJB11 | 0 | ||
| ko04120 | Ubiquitin mediated proteolysis | 0.0277 | 4 | XLOC_024865;XLOC_018298;XLOC_021649;XLOC_025981 | UBE2B;HERC4;UBE2H;BT.19212 | 1 | XLOC_025357 | KEAP1 |
| ko0970 | Aminoacyl-tRNA biosynthesis | 0.0312 | 1 | XLOC_025065 | RARS | |||
| ko03010 | Ribosome | 0.0201 | 1 | XLOC_028013 | RPS23 | |||
| ko03008 | Ribosome biogenesis in eukaryotes | 0.0219 | 2 | XLOC_001726; XLOC_010292 | FCF1;UTP6 | 3 | XLOC_025000;XLOC_023340;XLOC_026685 | TCOF1;RRP7A;NOL6 |
| ko03040 | Spliceosome | 0.0388 | 11 | XLOC_000309;XLOC_004289;XLOC_007964;XLOC_012182;XLOC_012566;XLOC_017604;XLOC_019531;XLOC_021421;XLOC_023325;XLOC_025841;XLOC_028252 | SNRPB2;TRA2B;SMNDC1;TRA2A;BCAS2;SF3B1;PHF5A;BT.59135;SLU7;BT.91058;BT.91058;PLRG1 | 1 | XLOC_012196 | SFRS4 |
| ko03050 | Proteasome | 0.0142 | 7 | XLOC_001624;XLOC_001843;XLOC_003577;XLOC_004136;XLOC_012473;XLOC_020934;XLOC_021072 | BT.22570;PSMD14;PSMA3;BT.56882;PSMA2;POMP;PSMC2 | |||
| ko04142 | Lysosome | 0.0394 | 0 | 5 | XLOC_001832;XLOC_006153;XLOC_010442;XLOC_012190;XLOC_013979 | BT.35140; LAPTM5; ARSB; CD68; CTSH | ||
| ko04150 | mTOR signaling pathway | 0.0300 | 1 | XLOC_018127 | DDIT4 | 1 | XLOC_013054; | RICTOR |
| ko04350 | TGF-beta signaling pathway | 0.0190 | 2 | XLOC_003540;XLOC_018178 | ID2;BT.48514 | 3 | XLOC_004021;XLOC_004591;XLOC_013257 | FST;ID1;TFDP1 |
| ko04115 | p53 signaling pathway | 0.0247 | 5 | XLOC_007111;XLOC_012771;XLOC_025054;XLOC_026769;XLOC_026996 | GADD45G;SESN1;BT.36413;SESN2;CCNG1 | 2 | XLOC_021046;XLOC_018555 | IGFBP3;BT.33239 |
| ko04310 | Wnt signaling pathway | 0.0458 | 1 | XLOC_007394 | CACYBP | 1 | XLOC_007966 | SFRP2 |
| ko03050 | Proteasome | 0.0142 | 7 | XLOC_001624;XLOC_001843;XLOC_003577;XLOC_004136;XLOC_012473;XLOC_020934;XLOC_021072 | BT.22570;PSMD14;PSMA3;BT.56882;PSMA2;POMP;PSMC2 |