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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)

From: Understanding the regulatory mechanisms of milk production using integrative transcriptomic and proteomic analyses: improving inefficient utilization of crop by-products as forage in dairy industry

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