Table 2 Gene set enrichment analysis– single nucleotide polymorphism results for conception rate to first service (CCR1) in Holstein cows

Cell Cycle, Mitotic (R-HSA-69278)

300 (93)

RAD21, PAFAH1B1, CEP290, CLIP1, RBL2, TUBB4B, CENPH, CCNB1, CDK6, CCNE2, CEP250, CENPJ, CASC5, PRIM2, KNTC1, CDK1, YWHAE, CLASP1, BTRC, CDC14A, SDCCAG8, CDK7, CDKN2A, CDKN2B, CEP41, CCNA2, NUF2, KIF23, PSMA4, PSMB8, PSMB9, MCM7, MCM3, MCM2, UBE2C, OFD1, RPA3, KIF2B, NUP133, AHCTF1, PRKAR2B, NUDC, PRIM1, TYMS, ALMS1, CENPT, ANAPC5, CEP72, CEP70, CUL1, DHFR, ANAPC7, SKA1, AKAP9, NINL, PRKACA, STAG2, CDC45, CCNE1, PLK1, PSMD11, DYRK1A, CDT1, PSMB7, ITGB3BP, MAD1L1, NUMA1, INCENP, CEP135, RBL1, FBXO5, PPP2R5E, ANAPC10, DCTN1, Sect. 13, PSMB10, CDC7, PTTG1, BUB1B, CENPP, BUB1, PSMA2, LIN52, PSME1, PSME2, TUBGCP3, FGFR1OP, PSMB2, PPP2R2A, PSMC1, RB1, YWHAG, CCND2

Cell Cycle (R-HSA-1640170)

364 (126)

RAD21, PAFAH1B1, CEP290, CLIP1, RBL2, TUBB4B, CENPH, CCNB1, CDK6, RFWD2, SYNE2, H2AFX, CCNE2, CEP250, CENPJ, CASC5, PRIM2, KNTC1, CDK1, YWHAE, CLASP1, BTRC, CDC14A, SDCCAG8, CDK7, CDKN2A, CDKN2B, CEP41, CCNA2, NUF2, RUVBL1, KIF23, PSMA4, POT1, PSMB8, PSMB9, MCM7, MCM3, ATR, MCM2, UBE2C, OFD1, HIST1H4D, RPA3, KIF2B, NUP133, AHCTF1, PRKAR2B, SYNE1, NUDC, PRIM1, TYMS, ALMS1, CENPT, ANAPC5, CEP72, CEP70, CUL1, FKBP6, DHFR, ANAPC7, SKA1, HIST1H2BN, SMC1B, AKAP9, NINL, PRKACA, STAG2, CDC45, CCNE1, PLK1, PSMD11, DYRK1A, MIS18A, RAD1, CDT1, PSMB7, ITGB3BP, MAD1L1, NUMA1, INCENP, HUS1, CEP135, RBL1, FBXO5, PPP2R5E, ANAPC10, DCTN1, Sect. 13, PSMB10, CDC7, PTTG1, BUB1B, CENPP, BUB1, PSMA2, LIN52, PSME1, PSME2, TUBGCP3, FGFR1OP, PSMB2, PPP2R2A, PSMC1, RB1, YWHAG, CCND2, HIST1H2BI, REC8, CEP76, HJURP, CHEK2, HIST1H2BJ, PSMC6, HIST3H2BB, RSF1, GINS4, MCM8, ORC2, PCNT, LIN54, ANAPC1, PSMC2, HIST1H2BB, ANAPC2, SSNA1

Protein Polymerization (GO:0051258)

79 (21)

TWF1, TUBB4B, ARFIP2, TUBA8, CAPZA2, F2, SCIN, WASF1, SLAIN2, ANG, VIL1, CAPZB, TMSB4, RASA1, SNCA, ARPIN, ARPC1A, UBE2C, RAC1, WASL, ARPC5

Recruitment of Mitotic Centrosome Proteins and Complexes

(R-HSA-380270)

62 (22)

PAFAH1B1, CEP290, TUBB4B, CCNB1, CEP250, CENPJ, CDK1, YWHAE, CLASP1, SDCCAG8, CEP41, OFD1, PRKAR2B, ALMS1, CEP72, CEP70, AKAP9, NINL, PRKACA, PLK1, NUMA1, CEP135

Mitotic G2-G2/M phases

(R-HSA-453274)

76 (24)

PAFAH1B1, CEP290, TUBB4B, CCNB1, CEP250, CENPJ, CDK1, YWHAE, CLASP1, SDCCAG8, CDK7, CEP41, CCNA2, OFD1, PRKAR2B, ALMS1, CEP72, CEP70, AKAP9, NINL, PRKACA, PLK1, NUMA1, CEP135

Loss of NLP From Mitotic Centrosomes (R-HSA-380259)

55 (20)

PAFAH1B1, CEP290, TUBB4B, CEP250, CENPJ, CDK1, YWHAE, CLASP1, SDCCAG8, CEP41, OFD1, PRKAR2B, ALMS1, CEP72, CEP70, AKAP9, NINL, PRKACA, PLK1, CEP135

Cellular Component Disassembly (GO:0022411)

81 (20)

TWF1, DPP4, MICAL3, CCNB1, GABARAPL1, MMP13, CAPZA2, SCIN, VIL1, CAPZB, ENDOG, FOXL2, BAX, KIF2B, FIS1, NAPB, STMN1, DSTN, SBDS, MTRF1L

Macromolecular Complex Assembly (GO:0065003)

372 (84)

TWF1, SRSF1, TUBB4B, CNOT7, HES1, SF3A1, H1FOO, CENPH, CHMP4A, DPAGT1, CAMK2D, KCTD1, SAMHD1, VAMP4, ARFIP2, RAD51, SRR, TUBA8, SLC6A4, CAPZA2, TBCA, OAT, F2, FECH, SCIN, WASF1, SLAIN2, ANG, VIL1, PEX5, VWF, STRAP, EIF6, COX7A2L, CAPZB, SNAP29, MGST1, TMSB4, RASA1, IGF1R, GEMIN8, LRRC6, NAP1L1, CBR4, SNCA, NUDT21, ARPIN, COX19, ARPC1A, ASF1A, UBE2C, NLRC4, NDUFAF6, MICU1, CLU, BAX, LMO4, RAC1, CAT, WASL, ARPC5, FIS1, NAPB, PRPF19, CYBA, SBDS, DRC1, LONP1, ARPC3, TARBP2, PDCL, IL5, H4, HIST1H1A, ATP6V0A2, PSMD11, RDX, ARL6, MIS18A, FAS, LUC7L3, KCTD5, SAR1A, MIF

Signaling by NGF (R-HAS-9031628)

207(80)

NTRK2, SOS2, APH1B, RAP1A, PRKCE, ADCY2, ADCY5, ATF1, VAV3, MAPK8, AKT3, MYD88, SORCS3, CDK1, AKAP13, ADAM17, YWHAE, MCF2, TIAM2, CAMK4, TIAM1, PRKCI, FOXO3, ADCY1, DUSP6, FGD2, ADCY9, SQSTM1, FGD4, ABR, PIK3R1, NR4A1, ITSN1, PDPK1, OBSCN, RALB, MEF2A, PDE1A, AP2A1, PRKAR2A, RAC1, RPS6KA3, CHUK, KIDINS220, AP2B1, PRKAR2B, FURIN, ADCYAP1R1, PIK3CB, RASGRF2, ARHGEF3, SRC, ARHGAP4, MAPKAP1, PHLPP1, SHC3, CASP9, FGD3, LINGO1, ARHGEF6, PRKACA, MAP2K5, ITPR3, ADCY8, ADCY7, ITGB3BP, MEF2C, TRIO, FOXO1, PLCG1, AKT1S1, MTOR, PIK3CA, CLTC, CLTA, RIPK2, ADCY3, TRAF6, PRKAR1B, APH1A

Protein Complex Assembly (GO:0065003)

303 (73)

TWF1, TUBB4B, HES1, H1FOO, CENPH, CHMP4A, DPAGT1, CAMK2D, KCTD1, SAMHD1, VAMP4, ARFIP2, RAD51, SRR, TUBA8, SLC6A4, CAPZA2, TBCA, OAT, F2, SCIN, WASF1, SLAIN2, ANG, VIL1, PEX5, VWF, COX7A2L, CAPZB, SNAP29, MGST1, TMSB4, RASA1, IGF1R, LRRC6, NAP1L1, CBR4, SNCA, NUDT21, ARPIN, COX19, ARPC1A, ASF1A, UBE2C, NLRC4, NDUFAF6, MICU1, CLU, BAX, LMO4, RAC1, CAT, WASL, ARPC5, FIS1, NAPB, CYBA, DRC1, LONP1, ARPC3, PDCL, IL5, H4, HIST1H1A, ATP6V0A2, PSMD11, RDX, ARL6, MIS18A, FAS, KCTD5, SAR1A, MIF

Regulation of RNA Splicing (GO:0043484)

33 (13)

SRSF1, SF3A1, RBFOX1, CLK3, SNW1, HNRNPF, SNRNP70, PIK3R1, RBM22, CELF3, RBFOX2, PRPF19, NSRP1

Actin Filament Polymerization (GO:0030041)

48 (15)

TWF1, ARFIP2, CAPZA2, SCIN, WASF1, ANG, VIL1, CAPZB, TMSB4, RASA1, ARPIN, ARPC1A, RAC1, WASL, ARPC5

Actin Polymerization or Depolymerization (GO:0008154)

58 (17)

TWF1, MICAL3, ARFIP2, CAPZA2, SCIN, WASF1, ANG, VIL1, CAPZB, TMSB4, RASA1, ARPIN, ARPC1A, RAC1, WASL, ARPC5, DSTN

Cilium Morphogenesis (GO:0060271)

46 (8)

CEP290, ASAP1, IFT46, IFT43, TTLL1, C7H5ORF30, CEP41, LRRC6

Protein Complex Biogenesis (GO:0070271)

306 (73)

TWF1, TUBB4B, HES1, H1FOO, CENPH, CHMP4A, DPAGT1, CAMK2D, KCTD1, SAMHD1, VAMP4, ARFIP2, RAD51, SRR, TUBA8, SLC6A4, CAPZA2, TBCA, OAT, F2, SCIN, WASF1, SLAIN2, ANG, VIL1, PEX5, VWF, COX7A2L, CAPZB, SNAP29, MGST1, TMSB4, RASA1, IGF1R, LRRC6, NAP1L1, CBR4, SNCA, NUDT21, ARPIN, COX19, ARPC1A, ASF1A, UBE2C, NLRC4, NDUFAF6, MICU1, CLU, BAX, LMO4, RAC1, CAT, WASL, ARPC5, FIS1, NAPB, CYBA, DRC1, LONP1, ARPC3, PDCL, IL5, H4, HIST1H1A, ATP6V0A2, PSMD11, RDX, ARL6, MIS18A, FAS, KCTD5, SAR1A, MIF

Macromolecular Complex Binding (GO:0044877)

297 (97)

PAFAH1B1, RAP1A, H1FOO, PPARGC1A, CENPH, GABARAPL1, MMP13, MUM1, SLC6A4, YWHAE, PLS1, MYO10, F2, STRN3, COLEC12, SCIN, WASF1, SEC61A2, MYB, HMGB4, TDRD3, GNAO1, VIL1, VWF, EIF6, PRKCB, CAPZB, GNAI1, TFAM, POLR3A, IGF1R, SEC61A1, DNAJC2, HMGN4, PIK3R1, USH1C, PDGFA, MEF2A, ARPC1A, ASF1A, PRIMPOL, LMO2, MYO1D, NANOG, MTA3, CCNT1, TNNC1, MTM1, KIF2B, MSR1, MEN1, KDM8, ZNHIT1, PPIH, SCARB1, SBDS, NR5A1, CDC5L, SPARC, PLAC8, ARPC3, MSH2, SKA1, RNF169, FBLN5, RNF20, HIST1H1A, THBS4, GNAT3, ITGB6, PLK1, BAP1, RBPJ, ANKRD54, CETN1, FOXP1, KCTD5, MEF2C, FSCN2, UHRF1, MCMBP, HMGN3, GNB1, ERMN, GNAT1, REEP4, MAP1LC3B, ASPN, CITED2, AAK1, TMOD1, ITGB1, ARPC1B, URI1, PPARG, SPDL1, MYL12A

Cellular Protein Complex Disassembly (GO:0032984)

40 (13)

TWF1, MICAL3, CCNB1, CAPZA2, SCIN, VIL1, CAPZB, KIF2B, NAPB, STMN1, DSTN, SBDS, MTRF1L

Cellular Macromolecular Complex Assembly (GO:0006461)

245 (55)

TWF1, SRSF1, TUBB4B, CNOT7, SF3A1, H1FOO, CENPH, VAMP4, ARFIP2, TUBA8, CAPZA2, TBCA, F2, SCIN, WASF1, SLAIN2, ANG, VIL1, STRAP, EIF6, COX7A2L, CAPZB, SNAP29, TMSB4, RASA1, GEMIN8, LRRC6, NAP1L1, SNCA, ARPIN, COX19, ARPC1A, ASF1A, UBE2C, NDUFAF6, RAC1, WASL, ARPC5, NAPB, PRPF19, CYBA, SBDS, DRC1, LONP1, ARPC3, TARBP2, H4, HIST1H1A, ATP6V0A2, PSMD11, RDX, ARL6, MIS18A, LUC7L3, SAR1A

Regulation of Actin Filament Polymerization (GO:0030833)

44 (6)

TWF1, CAPZA2, SCIN, VIL1, CAPZB, TMSB4