Table 4.
Top 10 enriched gene ontology terms for the genes selected which better classify high- and low-RFI animals based on the expression in the rumen tissue in the sPLS-DA for Angus, Charolais and Kinsella breeds.
| Breed | Description | GO class | P-value | FDR | Gene |
|---|---|---|---|---|---|
| Angus | Contractile fiber | CC | 3.18 × 10−53 | 9.82 × 10−51 | MYH15, FBXO32, SCN1A, CASQ2, MYH6, KY, LMOD3, MYOZ3, TNNT3, ANKRD1, LMOD2, SYNPO2L, TRIM54, MYOZ1, MYPN, MYBPC1, RYR1, MYL2, TNNC1, MYH2, STYXL2, CMYA5, MYL3, CSRP3, MYOT, TNNI2, LRRC39, XIRP2, NRAP, TNNT1, IGFN1, ACTA1, MYLPF, ABRA, MYOM2, CAV3, TNNC2, LDB3, MYL1, ACTN3, MYOM3, MYH1, NEB, MYLK2, CASQ1, ACTN2, CACNA1S, MYOM1, KLHL41, TCAP, SMTNL1, TRIM63, CAPN3, TNNI1, MYH8, FLNC, TMOD4, MYOD1, MYOZ2 |
| Angus | Myofibril | CC | 5.05 × 10−53 | 9.82 × 10−51 | MYH15, FBXO32, SCN1A, CASQ2, MYH6, KY, LMOD3, MYOZ3, TNNT3, ANKRD1, LMOD2, SYNPO2L, TRIM54, MYOZ1, MYPN, MYBPC1, RYR1, MYL2, TNNC1, MYH2, STYXL2, CMYA5, MYL3, CSRP3, MYOT, TNNI2, LRRC39, XIRP2, NRAP, TNNT1, IGFN1, ACTA1, ABRA, MYOM2, CAV3, TNNC2, LDB3, MYL1, ACTN3, MYOM3, MYH1, NEB, MYLK2, CASQ1, ACTN2, CACNA1S, MYOM1, KLHL41, TCAP, SMTNL1, TRIM63, CAPN3, TNNI1, MYH8, FLNC, TMOD4, MYOD1, MYOZ2 |
| Angus | Sarcomere | CC | 3.81 × 10−51 | 4.94 × 10−49 | FBXO32, SCN1A, CASQ2, MYH6, KY, LMOD3, MYOZ3, TNNT3, ANKRD1, LMOD2, SYNPO2L, TRIM54, MYOZ1, MYPN, RYR1, MYL2, TNNC1, MYH2, STYXL2, CMYA5, MYL3, CSRP3, MYOT, TNNI2, LRRC39, XIRP2, NRAP, TNNT1, IGFN1, ACTA1, ABRA, MYOM2, CAV3, TNNC2, LDB3, MYL1, ACTN3, MYOM3, MYH1, NEB, MYLK2, CASQ1, ACTN2, CACNA1S, MYOM1, KLHL41, TCAP, SMTNL1, TRIM63, CAPN3, TNNI1, MYH8, FLNC, TMOD4, MYOZ2 |
| Angus | Muscle system process | BP | 7.53 × 10−37 | 2.22 × 10−33 | STAC2, FBXO32, SLC8A3, SCN1A, SGCA, CLCN1, CASQ2, MYH6, TRIM72, LMOD3, CHRM3, CKMT2, MYBPH, TNNT3, LMOD2, SCN4B, MYOZ1, MYBPC1, RYR1, MYL2, TNNC1, MYH2, MYL3, CSRP3, MYOT, TNNI2, TNNT1, MYBPC2, ACTA1, MYLPF, MYOM2, CAV3, TNNC2, ATP2A1, MYL1, ACTN3, MYOM3, MYH1, MYLK2, CASQ1, SLN, PGAM2, ACTN2, CACNA1S, MYOM1, KLHL41, JSRP1, TCAP, GHSR, TRIM63, SCN4A, TNNI1, MYH8, TMOD4, CHRNA1, MYOD1, MLIP, MYOZ2, TACR2 |
| Angus | Muscle contraction | BP | 3.20 × 10−35 | 4.72 × 10−32 | STAC2, SLC8A3, SCN1A, SGCA, CLCN1, CASQ2, MYH6, LMOD3, CHRM3, CKMT2, MYBPH, TNNT3, LMOD2, SCN4B, MYBPC1, RYR1, MYL2, TNNC1, MYH2, MYL3, CSRP3, MYOT, TNNI2, TNNT1, MYBPC2, ACTA1, MYLPF, MYOM2, CAV3, TNNC2, ATP2A1, MYL1, ACTN3, MYOM3, MYH1, MYLK2, CASQ1, PGAM2, ACTN2, CACNA1S, MYOM1, KLHL41, JSRP1, TCAP, GHSR, TRIM63, SCN4A, TNNI1, MYH8, TMOD4, CHRNA1, TACR2 |
| Angus | Myofibril assembly | BP | 6.47 × 10−30 | 6.36 × 10−27 | SIX4, MYH6, LMOD3, TNNT3, ANKRD1, LMOD2, SYNPO2L, MYOZ1, MYPN, MYL2, CSRP3, NRAP, TNNT1, ACTA1, MYOM2, CAV3, LDB3, NEB, CASQ1, ACTN2, KLHL41, TCAP, CAPN3, FLNC, TMOD4, MYOZ2 |
| Angus | Striated muscle cell development | BP | 1.04 × 10−29 | 7.69 × 10−27 | SIX4, MYH6, LMOD3, TNNT3, ANKRD1, LMOD2, SYNPO2L, MYOZ1, MYPN, MYL2, CSRP3, NRAP, TNNT1, ACTA1, MYOM2, CAV3, LDB3, NEB, CASQ1, ACTN2, KLHL41, TCAP, CAPN3, FLNC, TMOD4, MYOZ2 |
| Angus | I band | CC | 1.27 × 10−26 | 1.23 × 10−24 | FBXO32, SCN1A, CASQ2, MYH6, KY, MYOZ3, ANKRD1, SYNPO2L, TRIM54, MYOZ1, MYPN, RYR1, MYL3, CSRP3, MYOT, XIRP2, NRAP, IGFN1, CAV3, LDB3, ACTN3, NEB, CASQ1, ACTN2, CACNA1S, TCAP, SMTNL1, TRIM63, CAPN3, FLNC, MYOZ2 |
| Angus | Muscle cell development | BP | 2.77 × 10−25 | 1.63 × 10−22 | NFATC2, SIX4, MYH6, SYPL2, LMOD3, TNNT3, ANKRD1, LMOD2, SYNPO2L, MYF6, ALPK2, MYOZ1, MYPN, RYR1, MYL2, CSRP3, NRAP, TNNT1, ACTA1, MYOM2, CAV3, LDB3, ACTN3, NEB, CASQ1, ACTN2, KLHL41, TCAP, CAPN3, FLNC, TMOD4, MYOD1, MYOZ2 |
| Angus | Sarcomere organization | BP | 4.48 × 10−25 | 2.20 × 10−22 | SIX4, MYH6, TNNT3, ANKRD1, LMOD2, SYNPO2L, MYOZ1, MYPN, CSRP3, TNNT1, MYOM2, CAV3, LDB3, CASQ1, ACTN2, KLHL41, TCAP, CAPN3, FLNC, MYOZ2 |
| Charolais | Voltagx10-gated potassium channel activity | MF | 5.29 × 10−05 | 0.022 | KCNK9, KCNH3, HCN3, LRRC55, KCNA2, KCNB1, KCNJ13 |
| Charolais | Voltagx10-gated cation channel activity | MF | 1.56 × 10−04 | 0.022 | KCNK9, KCNH3, HCN3, LRRC55, KCNA2, CACNG1, KCNB1, KCNJ13 |
| Charolais | Voltagx10-gated ion channel activity | MF | 3.10 × 10−04 | 0.022 | KCNK9, KCNH3, HCN3, LRRC55, SCN4A, KCNA2, CACNG1, KCNB1, KCNJ13 |
| Charolais | Voltagx10-gated channel activity | MF | 3.10 × 10−04 | 0.022 | KCNK9, KCNH3, HCN3, LRRC55, SCN4A, KCNA2, CACNG1, KCNB1, KCNJ13 |
| Charolais | Potassium channel activity | MF | 3.16 × 10−04 | 0.022 | KCNK9, KCNH3, HCN3, LRRC55, KCNA2, KCNB1, KCNJ13 |
| Charolais | Tachykinin receptor activity | MF | 3.35 × 10−04 | 0.022 | TACR1, TACR2 |
| Charolais | Cation channel activity | MF | 3.39 × 10−04 | 0.022 | KCNK9, KCNH3, HCN3, LRRC55, SCN4A, MCOLN3, KCNA2, CACNG1, KCNB1, KCNJ13, PKD1L2, NALF1 |
| Charolais | Receptor ligand activity | MF | 7.78 × 10−04 | 0.044 | IL6, EPGN, IL17B, SPP1, F2, CCL27, FGF5, IL37, XCL1, SST, TAFA4, CARTPT, LTB, IL27 |
| Charolais | Signaling receptor activator activity | MF | 8.92 × 10−04 | 0.045 | IL6, EPGN, IL17B, SPP1, F2, CCL27, FGF5, IL37, XCL1, SST, TAFA4, CARTPT, LTB, IL27 |
| Charolais | Gated channel activity | MF | 0.001 | 0.049 | KCNK9, KCNH3, HCN3, LRRC55, SCN4A, MCOLN3, KCNA2, CACNG1, KCNB1, KCNJ13, NALF1 |
| Kinsella | Contractile fiber | CC | 1.82 × 10−38 | 7.88 × 10−36 | MYH4, MYPN, MYL6B, KY, MYOZ2, CAPN3, LMOD3, IGFN1, TNNT1, TNNI1, CACNA1S, TNNC1, CAV3, TNNC2, CSRP3, MYLPF, MYL2, TMOD4, LRRC39, MYL1, NEB, MYH1, MYH7, MYOM2, ACTN3, MYOT, TNNT3, TNNI2, MYL3, MYOZ1, SMTNL1, MYBPC1, ACTA1, MYH2, NRAP, RYR1, CASQ1, LMOD2, TRIM54, XIRP2, MYH8, LDB3, ANKRD1, CAVIN4, MYLK2, SYNPO2L, CMYA5, CASQ2, MYH6 |
| Kinsella | Sarcomere | CC | 1.56 × 10−37 | 3.39 × 10−35 | MYH4, MYPN, KY, MYOZ2, CAPN3, LMOD3, IGFN1, TNNT1, TNNI1, CACNA1S, TNNC1, CAV3, TNNC2, CSRP3, MYL2, TMOD4, LRRC39, MYL1, NEB, MYH1, MYH7, MYOM2, ACTN3, MYOT, TNNT3, TNNI2, MYL3, MYOZ1, SMTNL1, ACTA1, MYH2, NRAP, RYR1, CASQ1, LMOD2, TRIM54, XIRP2, MYH8, LDB3, ANKRD1, CAVIN4, MYLK2, SYNPO2L, CMYA5, CASQ2, MYH6 |
| Kinsella | Myofibril | CC | 6.20 × 10−37 | 8.95 × 10−35 | MYH4, MYPN, KY, MYOZ2, CAPN3, LMOD3, IGFN1, TNNT1, TNNI1, CACNA1S, TNNC1, CAV3, TNNC2, CSRP3, MYL2, TMOD4, LRRC39, MYL1, NEB, MYH1, MYH7, MYOM2, ACTN3, MYOT, TNNT3, TNNI2, MYL3, MYOZ1, SMTNL1, MYBPC1, ACTA1, MYH2, NRAP, RYR1, CASQ1, LMOD2, TRIM54, XIRP2, MYH8, LDB3, ANKRD1, CAVIN4, MYLK2, SYNPO2L, CMYA5, CASQ2, MYH6 |
| Kinsella | Muscle system process | BP | 2.94 × −29 | 1.04 × 10−25 | STAC2, MYH4, CHRM2, SSTR2, PRKAG3, MYL6B, MLIP, STAC3, P2RX2, MYOZ2, LMOD3, TNNT1, TNNI1, CACNA1S, SCN4A, TRIM72, SLN, TNNC1, CAV3, ATP2A1, TNNC2, CSRP3, MYLPF, MYL2, MYBPC2, TMOD4, MYL1, MYBPH, MYH1, MYH7, MYOM2, ACTN3, MYOT, TNNT3, TNNI2, MYL3, MYOZ1, MYBPC1, ACTA1, MYH2, CHRNA1, RYR1, CASQ1, LMOD2, MYH8, CLCN1, JSRP1, MYLK2, CKMT2, CASQ2, MYH6, SCN4B, MSTN |
| Kinsella | Muscle contraction | BP | 1.60 × 10−27 | 2.86 × 10−24 | STAC2, MYH4, CHRM2, SSTR2, MYL6B, STAC3, P2RX2, LMOD3, TNNT1, TNNI1, CACNA1S, SCN4A, TNNC1, CAV3, ATP2A1, TNNC2, CSRP3, MYLPF, MYL2, MYBPC2, TMOD4, MYL1, MYBPH, MYH1, MYH7, MYOM2, ACTN3, MYOT, TNNT3, TNNI2, MYL3, MYBPC1, ACTA1, MYH2, CHRNA1, RYR1, CASQ1, LMOD2, MYH8, CLCN1, JSRP1, MYLK2, CKMT2, CASQ2, MYH6, SCN4B |
| Kinsella | Myofibril assembly | BP | 1.75 × 10−21 | 2.07 × 10−18 | MYPN, MYOZ2, CAPN3, LMOD3, TNNT1, CAV3, CSRP3, MYL2, TMOD4, NEB, MYOM2, TNNT3, MYOZ1, ACTA1, NRAP, CASQ1, LMOD2, LDB3, ANKRD1, SYNPO2L, MYH6 |
| Kinsella | Striated muscle cell development | BP | 2.51 × 10−21 | 2.23 × 10−18 | MYPN, MYOZ2, CAPN3, LMOD3, TNNT1, CAV3, CSRP3, MYL2, TMOD4, NEB, MYOM2, TNNT3, MYOZ1, ACTA1, NRAP, CASQ1, LMOD2, LDB3, ANKRD1, SYNPO2L, MYH6 |
| Kinsella | I band | CC | 1.08 × 10−19 | 1.17 × 10−17 | MYPN, KY, MYOZ2, CAPN3, IGFN1, CACNA1S, CAV3, CSRP3, NEB, MYH7, ACTN3, MYOT, MYL3, MYOZ1, SMTNL1, NRAP, RYR1, CASQ1, TRIM54, XIRP2, LDB3, ANKRD1, CAVIN4, SYNPO2L, CASQ2, MYH6 |
| Kinsella | Skeletal muscle contraction | BP | 1.64 × 10−19 | 1.17 × 10−16 | STAC2, STAC3, TNNT1, TNNI1, SCN4A, TNNC1, CAV3, ATP2A1, TNNC2, MYH7, ACTN3, TNNT3, TNNI2, CHRNA1, CASQ1, MYH8, JSRP1 |
| Kinsella | Muscle cell development | BP | 7.61 × 10−19 | 4.52 × 10−16 | SHOX2, TBX18, MYPN, STAC3, ALPK2, P2RX2, MYOZ2, CAPN3, LMOD3, TNNT1, CAV3, CSRP3, MYL2, TMOD4, NEB, MYOM2, ACTN3, TNNT3, MYOZ1, ACTA1, NRAP, RYR1, CASQ1, LMOD2, LDB3, ANKRD1, SYNPO2L, MYH6 |