Table 3 Relevant and significantly enriched biological functions (KEGG pathways) for diversity of muscle expression for five pig breeds

Signaling pathways

Focal adhesion

27

1.8E-08

ITGA1, MAPK1, comP, ITGA6, ERBB2, LAMA2, CCND2, BCAR1, DIAPH1, PTEN, ITGA2, SPP1, ACTB, LAMC1, CAPN2, COL4A1, EGFR, VAV2, THBS4, ITGA9, THBS2, PTK2, PIK3CG, VEGFA, fn1, PPP1CB, VAV3

Regulation of actin cytoskeleton

27

3.5E-08

PIP4K2A, ITGA1, MAPK1, ARPC2, ITGA6, ITGB2, ARPC1B, F2R, BCAR1, DIAPH1, GNA12, ITGA2, NCKAP1L, GSN, ACTB, TMSB4X, EGFR, VAV2, ITGA9, CD14, PTK2, Kras, BAIAP2, PIK3CG, fn1, PPP1CB, VAV3

ECM-receptor interaction

14

5.8E-06

ITGA1, comP, ITGA6, LAMA2, ITGA2, GP1BB, SPP1, LAMC1, COL4A1, THBS4, ITGA9, THBS2, AGRN, fn1

Adherens junction

12

2.7E-05

MAPK1, PARD3, CTNNA3, ACP1, ERBB2, PTPRJ, ACTB, EGFR, BAIAP2, CREBBP, SORBS1, PVRL3

Metabolic pathways

Valine, leucine and isoleucine degradation

12

2.3E-07

ALDH3A2, BCAT1, OXCT1, EHHADH, IVD, BCKDHB, ECHS1, ACADSB, HADHA, PCCB, AUH, ALDH2

Lysine degradation

9

0.0002

MLL5, ALDH3A2, EHHADH, NSD1, WHSC1L1, ECHS1, HADHA, setmar, ALDH2

Purine metabolism

16

0.00033

NUDT2, Pgm2, GMPR2, POLR2G, ENPP1, RRM2B, FHIT, GUCY1A3, ADA, NT5C2, NME6, PGM1, PRPS2, ATIC, NT5E, POLR3E

beta-Alanine metabolism

6

0.00088

ALDH3A2, EHHADH, ECHS1, CARNS1, HADHA, ALDH2

Arginine and proline metabolism

8

0.0014

ALDH3A2, ACY1, P4HA1, GLUD1, CARNS1, AMD1, ALDH4A1, ALDH2

Fatty acid metabolism

7

0.0014

ALDH3A2, EHHADH, ECHS1, ACADSB, ACSL4, HADHA, ALDH2

Cellular processes

Phagosome

21

9.2E-08

comP, CTSS, ATP6V1C1, ITGB2, ITGA2, PIK3C3, ACTB, CYBB, CYBA, TFRC, THBS4, CD14, THBS2, NCF4, NCF2, DYNC1I2, EEA1, FCGR2B, MRC1, TUBA8, TUBA4A

Protein processing in endoplasmic reticulum

21

7E-07

nsfl1c, BAG2, UBE4B, PARK2, SAR1B, HSPH1, SEC24D, DNAJC1, CAPN2, DDOST, BCAP31, HSPA2, PDIA3, CUL1, UBE2D4, HERPUD1, EDEM2, DNAJA1, DERL1, CKAP4, TUSC3

mRNA surveillance pathway

13

0.000016

SAP18, PPP2R5A, CPSF6, CLP1, PPP2R2A, PAPOLA, PAPOLB, PPP2CB, Fip1l1, ETF1, HBS1L, CPSF3, CSTF2T

Endocytosis

20

3.61E-05

RAB11FIP5, PARD3, KIT, F2R, DNM2, EHD1, RABEP1, ARRB2, GRK5, DNM1L, FOLR1, EGFR, TFRC, HSPA2, WWP1, ZFYVE16, SMAP2, EEA1, epn1, FAM125B