Table 3.
Main overrepresented biological processes shared by genes selected as predictors of feed efficiency traits
| GO terms | Nb genes | E | P Value | Clustered genes |
|---|---|---|---|---|
| RFI (clustered pathways among 222 VIP) | ||||
| GO:0051270~regulation of cell motion | 12 | 3.35 | < 0.001 |
BCL2, F10, HBZGF, HDAC5, INS-IGF2, LAMA4, NTN1, NRP1, PIK3R1, PDGFRB, SERPINE2, TGFR3 |
| GO:0007167~enzyme linked receptor protein signaling pathway | 14 | 2.36 | < 0.001 | AMHR2, NRP1, INS-IGF2, TIPARP, TRIO, GRB10, UTP11L, PDGFRB, SPTBN1, HBEGF, ROR2, TGFBR3, ANGPTL1, PIK3R1 |
| GO:0001558~regulation of cell growth | 8 | 1.86 | 0.008 | NRP1, CD44, INS-IGF2, ABTB2, BCL2, HBEGF, NTN1, MAP 2 K5 |
| GO:0009725~response to hormone stimulus | 12 | 1.81 | 0.004 | HDAC5, PLA2G4A, AR, GRB10, CCND2, INS-IGF2, BCL2, NCOA6, TGFBR3, MGP, CA2, PIK3R1 |
| GO:0019318~hexose metabolic process | 8 | 1.79 | 0.008 | PDK1, TPI1, PHKB, INS-IGF2, UGDH, FUT2, SLC35A2, PMM1 |
| GO:0007517~muscle organ development | 8 | 1.79 | 0.01 | SRPK3, GATA6, TIPARP, PDGFRB, TGFBR3, HBEGF, ZFPM2, CBY1 |
| GO:0032844~regulation of homeostatic process | 5 | 1.38 | 0.05 | PLA2G4A, CD44, BCL2, RYR2, CA2 |
| GO:0060284~regulation of cell development | 10 | 1.33 | < 0.001 | HDAC5, NRP1, PSEN1, CCND2, INS-IGF2, BCL2, HOXD3, RTN4R, TGFBR3, NTN1 |
| GO:0048705~skeletal system morphogenesis | 7 | 1.31 | 0.004 | TULP3, PSEN1, HOXD3, TIPARP, PDGFRB, ROR2, MGP |
| GO:0006468~protein amino acid phosphorylation | 15 | 1.30 | 0.03 | SRPK3, PDK1, AMHR2, TWF1, TRIO, ADRBK1, CDKL2, PSEN1, BCL2, SPTBN1, ROR2, PDGFRB, TGFBR3, MERTK, MAP 2 K5 |
| GO:0010035~response to inorganic substance | 9 | 1.24 | 0.003 | ACTB, PLA2G4A, SLC1A3, BCL2, UROS, RYR2, MGP, ADRBK1, CA2 |
| GO:0006954~inflammatory response | 8 | 1.20 | 0.08 | HDAC5, CD44, INS-IGF2, FCN2, TICAM2, PSEN1, NLRP3, NFX1 |
| GO:0031667~response to nutrient levels | 8 | 1.10 | 0.08 | PLA2G4A, PSEN1, CD44, BCL2, RYR2, MGP |
| GO:0006650~glycerophospholipid metabolic process | 5 | 1.08 | 0.08 | PLA2G4A, ABHD5, ADNP, LPCAT2, PIK3R1 |
| GO:0016053~organic acid biosynthetic process | 6 | 1.08 | 0.04 | TPI1, SLC1A3, SCD, ABHD5, UROS, UGDH |
| FCR (clustered pathways among 267 VIP) | ||||
| GO:0007010~cytoskeleton organization | 13 | 2.4 | 0.001 | RND3, ACTC1, EZR, MACF1, CALD1, BCL2, SSH2, KRT8, ABI2, CNN1, TTN, PRKG1, EPB49 |
| GO:0007155~cell adhesion | 20 | 1.85 | 0.011 |
TECTA, NRP1, OLR1, GMDS, LGALS4, CNKSR3, NLGN3, CLDN10, CLDN11, CD84, RND3, LAMA4, EZR, ROBO1, COL27A1, BCL2, ACAN, MSN, PDZD2, EDA |
| GO:0060284~regulation of cell development | 8 | 1.78 | 0.038 | NRP1, LYN, ROBO1, INS-IGF2, BCL2, HOXD3, SMAD3, IGF2, NTN1 |
| GO:0006006~glucose metabolic process | 7 | 1.66 | 0.03 | TPI1, PYGM, PHKB, PYGL, INS-IGF2, SDS, UGDH, IGF2 |
| GO:0060537~muscle tissue development | 8 | 1.66 | 0.003 | MYF6, ACTC1, GATA6, TIPARP, TTN, CHRNA1, HOMER1, PTEN |
| GO:0005977~glycogen metabolic process | 3 | 1.61 | 0.099 | PYGM, PHKB, PYGL |
| GO:0000902~cell morphogenesis | 10 | 1.50 | 0.095 | EZR, NRP1, SEMA6C, MACF1, ROBO1, BCL2, LIFR, SOX6, NTN1, MYCBP2 |
| GO:0001568~blood vessel development | 9 | 1.42 | 0.034 | CCM2, LAMA4, NRP1, ROBO1, TIPARP, TGFA, DBH, FIGF, PTEN |
| GO:0045321~leukocyte activation | 8 | 1.35 | 0.077 | LYN, INS-IGF2, FYN, BCL2, SMAD3, MALT1, IGF2, HSPD1, ZNF3 |
| GO:0001501~skeletal system development | 10 | 1.29 | 0.055 | GNAQ, INS-IGF2, GFPT1, BCL2, HOXD3, TIPARP, ACAN, SMAD3, GNAS, IGF2, SOX6 |
| GO:0016052~carbohydrate catabolic process | 6 | 1.27 | 0.025 | GPD1L, OVGP1, TPI1, PYGM, PYGL, FUT1 |
| GO:0030163~protein catabolic process | 15 | 1.19 | 0.093 |
FEM1C, SOCS3, WWP1, USP9X, SOCS6, HECTD2, MALT1, ASB13, SMURF1, UBE2J2, SPOPL, UBE2Q1, USP32, MYCBP2, RNF111 |
| FCR (clustered pathways among 218 VIP) | ||||
| GO:0051270~regulation of cell motion | 15 | 1.95 | 0.001 | RET, MSH2, MDGA1, ARID5B, NR4A2, KDR, DSTN, IGSF8, MACF1, FYN, BAX, PAK4, FOXE1, THBS1, ACVR1 |
| GO:0034613~cellular protein localization | 13 | 1.58 | 0.004 | COPA, CLTA, YWHAZ, LTBP2, AP1G1, AKAP12, PTPRU, SYNGR1, MACF1, RPL23, BAX, CHM, RAB11A |
| GO:0006163~purine nucleotide metabolic process | 7 | 1.54 | 0.02 | ATP1B1, ENPP1, MSH2, ATP1B4, RAB11A, ACLY, MYH7 |
| GO:0001568~blood vessel development | 9 | 1.49 | 0.009 | EPAS1, BAX, CHM, ZFPM2, TNNI3, THBS1, MMP2, KDR, ACVR1 |
| GO:0006732~coenzyme metabolic process | 6 | 1.25 | 0.04 | DLD, ACLY, ALDH1L2, GCLM, MTHFD1L, MOCS1 |
| GO:0042592~homeostatic process | 17 | 1.22 | 0.02 | ENPP1, EPAS1, PTH1R, PRDX3, TNNI3, GCLM, MBP, KDR, RPS19, SLC4A11, RHCG, IL20RB, BAX, DLD, FABP4, IKBKB, CLN6 |
| GO:0003006~reproductive developmental process | 8 | 1.10 | 0.04 | HSPA2, MSH2, BAX, DLD, SF1, DHCR24, KDR, ACVR1 |
| GO:0048514~blood vessel morphogenesis | 7 | 1.08 | 0.04 | EPAS1, BAX, ZFPM2, TNNI3, THBS1, KDR, ACVR1 |
| GO:0043066~negative regulation of apoptosis | 11 | 1.04 | 0.01 | YWHAZ, MSH2, BAX, BTC, NR4A2, PRDX3, IKBKB, THBS1, GCLM, DHCR24, ACVR1 |
Very important genes (VIP) for prediction of feed efficiency traits (RFI: residual feed intake; FCR: feed conversion ratio; FCRe: net energy based-feed conversion ratio). Genes were clustered into functional groups using DAVID tool. The enrichment score (E > 1) for each cluster and P-value of the enrichment for the corresponding Gene Ontology (GO) terms are provided. Expression levels of genes indicated in bold font were further measured by qPCR