Table 2.
The KEGG pathway enrichment by up−/down-regulated proteins 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 Transcripts | ID of Increased Proteins | Gene Symbol of Increased Proteins | No. of Decreased Proteins | ID of Decreased Proteins | Gene Symbol of Decreased Proteins |
|---|---|---|---|---|---|---|---|---|
| ko03040 | Spliceosome | 0.0232 | 4 | IPI00687479;IPI00715218; IPI00702381; IPI00687395 | SNRNP40;LSM3; SNRPB;PRPF8 | 6 | IPI00690232;IPI00699558;IPI00687560;IPI00687015;IPI00717302; IPI00688521 | MAGOHB;SNRPD3;PCBP1;SNRPD2;SF3B4;BUD31 |
| ko04141 | Protein processing in endoplasmic reticulum | 0.0370 | 7 | IPI00702891;IPI00699038; IPI00693007; IPI00699107;IPI00691963; IPI00696616;IPI00688461 | ERP29; TXNDC5; DNAJC3;DNAJB11; CALR; SSR2; DNAJB1 | 1 | IPI00692963 | SEC23 |
| ko04974 | Protein digestion and absorption | 0.0101 | 0 | 7 | IPI00707857;IPI00708244;IPI00711933;IPI00712524;IPI00731432;IPI00826022;IPI00905045 | COL4A2; COL3A1; COL5A2; COL1A1; COL1A2;COL11A1; COL18A1 |
||
| ko04142 | Lysosome | 0.0314 | 2 | IPI00711862; IPI00706203 | NPC2; HEXB | 4 | IPI00697314;IPI00699372;IPI00717554;IPI00716195 | CTSC; ATP6V0A1; NAGLU; ATP6V0D1 |
| ko03010 | Ribosome | 0.0069 | 0 | 6 | IPI00695732;IPI00699146;IPI00707431;IPI00713536;IPI00714445;IPI00715091 | RPS2; RPS16; RPS20; RPS19; RPS12; RPS27 | ||
| ko00260 | Glycine, serine and threonine metabolism | 0.0090 | 1 | IPI00698589 | PGAM1 | 3 | IPI00698059;IPI00707303;IPI00715285 | SARDH; DMGDH; MAOA |
| ko04150 | mTOR signaling pathway | 0.0350 | 1 | IPI00700182 | EIF4B | 2 | IPI00903663; IPI00732002 | IKBKB; MAPK3 |
| ko03008 | Ribosome biogenesis in eukaryotes | 0.0374 | 2 | IPI00705941;IPI00708018 | REXO2; RAN | 1 | IPI00852474 | NAT10 |
| ko00280 | Valine, leucine and isoleucine degradation | 0.0468 | 3 | IPI00711918;IPI00717256;IPI00968674 | DBT; ACAT1; HMGCS1 | |||
| ko00380 | Tryptophan metabolism | 0.0381 | 1 | IPI00711918 | ACAT1 | 1 | IPI00698059 | MAOA |
| ko00330 | Arginine and proline metabolism | 0.0370 | 0 | 2 | IPI00698059;IPI00838420 | P4HA2; MAOA | ||
| ko00970 | Aminoacyl-tRNA biosynthesis | 0.0236 | 0 | 2 | IPI00689365;IPI00703906 | TARS2; AARS2 | ||
| ko00360 | Phenylalanine metabolism | 0.0473 | 0 | 1 | IPI00698059 | MAOA | ||
| ko00340 | Histidine metabolism | 0.0461 | 0 | 1 | IPI00698059 | MAOA | ||
| ko00350 | Tyrosine metabolism | 0.0365 | 0 | 1 | IPI00698059 | MAOA | ||
| ko00270 | Cysteine and methionine metabolism | 0.0432 | 1 | IPI00694739 | APIP | |||
| ko00010 | Glycolysis / Gluconeogenesis | 0.0302 | 3 | IPI00696912; IPI00698589; IPI00712164 | ACSS1; PGAM1; GALM | 2 | IPI00687211;IPI00715799 | HK1; GAPDHS |
| ko00190 | Oxidative phosphorylation | 0.0287 | 0 | 5 | IPI00697768;IPI00699372;IPI00712252;IPI00716163;IPI00716195 | ATPsynGL;ATP6V0A1; ATP5H;NDUFC1; ATP6V0D1 |
||
| ko00020 | Citrate cycle (TCA cycle) | 0.0399 | 2 | IPI00702781;IPI00708438 | IDH1; SUCLG1 | 1 | IPI00714468 | IDH2 |
| ko00640 | Propanoate metabolism | 0.0423 | 3 | IPI00696912;IPI00708438;IPI00711918 | ACSS1; ACAT1; SUCLG1 | |||
| ko00030 | Pentose phosphate pathway | 0.0352 | 2 | IPI00728589;IPI00904104 | TKT; RBKS | |||
| ko04146 | Peroxisome | 0.0169 | 4 | IPI00686601;IPI00702781;IPI00704382;IPI00714468 | SOD2; SCP2; IDH1; ECH1 | 1 | IPI00714468 | IDH2 |
| ko03320 | PPAR signaling pathway | 0.0263 | 4 | IPI00686601;IPI00699355;IPI00715548;IPI00839653 | SCP2; FABP4; APOA1; PPARD | |||
| ko04975 | Fat digestion and absorption | 0.0370 | 2 | IPI00695965;IPI00715548 | APOA4; APOA1 | 1 | IPI00710056 | APOB |
| ko04540 | Gap junction | 0.0352 | 0 | 2 | IPI00695917;IPI00732002 | MAPK3; GNAS | ||
| ko04210 | Apoptosis | 0.0261 | 1 | IPI00704835 | DFFA | 2 | IPI00709124; IPI00903663 | ENDOG; IKBKB |
| ko04151 | PI3K-Akt signaling pathway | 0.0301 | 1 | IPI00700182 | EIF4B | 9 | IPI00697595;IPI00707857;IPI00708244;IPI00712524;IPI00731432;IPI00732002;IPI00826022;IPI00903663;IPI00905045 | COL4A2; IKBKB; COL3A1; COL5A2; COL1A1; COL1A2; COL11A1; MAPK3; ITGA1 |
| ko04310 | Wnt signaling pathway | 0.0375 | 1 | IPI00708311 | CACYBP | 1 | IPI00699355 | PPARD |
| ko04350 | TGF-beta signaling pathway | 0.0272 | 0 | 1 | IPI00732002 | MAPK3 |