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Table 2 Assignment of DE-genes to canonical pathways in the comparison between breeds at either 63 dpc or 91 dpc

From: Gene expression analysis of mammary tissue during fetal bud formation and growth in two pig breeds – indications of prenatal initiation of postnatal phenotypic differences

Ingenuity Canonical Pathways PI vs. GL at 63 dpc or 91 dpc p-value1 Ratio2 Molecules
Clathrin-mediated Endocytosis Signaling 63 0.011 0.222 EPS15, STON2, CDC42, FGF2, ARPC5, NUMB, SH3GL2, ITGB8, PIK3R4, CD2AP, ACTR3, WASL, SNX9, IGF1, PIK3C3, ARPC3, DAB2, STAM, AAK1, PPP3CA, ACTA1, ATM, ITGB1, MYO6, ACTR2, PIK3C2A, SH3GL3, ACTB, CLTC, RAB7A, MET, CBL, SYNJ1, ARPC2, RAB11A, TFRC, UBC, PDGFD
91 0.106 0.029 EPS15, FGF2, TFRC, DAB2, AAK1
Corticotropin Releasing Hormone Signaling 63 0.033 0.204 RAP1B, PRKACB, RAF1, MAPK1, ARPC5, CREB5, PRKAG1, PRKD3, PRKCA, null, ITPR2, CNR1, PTCH1, GNAQ, GNAI1, ADCY6, MAPK12, RAP1A, ATF2, GNAS, GNAI3, PRKCI, MAPK14, PRKAR2B, PRKAG2, PRKCH, GLI1, PRKCB
91 0.258 0.022 PRKAR2B, ADCY3, PTGS2
Integrin Signaling 63 0.000 0.259 MAP2K4, RAP2B, RAF1, MYL2, MAPK1, ARPC5, ITGA8, KRAS, PIK3R4, PTEN, TSPAN3, RHOG, ARF4, CAV1, ITGAV, GSK3B, ACTA1, ATM, CAPN5, ACTR2, BCAR3, RAP1A, TTN, RHOQ, RND3, ARPC2, PPP1R12A, CAPN7, TSPAN6, RAP1B, FYN, PPP1CC, RALA, CDC42, PPP1CB, ITGB8, SHC1, ACTR3, WASL, RHOT1, PIK3C3, SOS1, ARPC3, ITGB1, PAK2, PIK3C2A, ASAP1, ACTB, ITGA2, MAPK8, ROCK1, WIPF1, ITGAX
91 0.191 0.024 RALA, ASAP1, ARF4, ITGA8, TTN
PI3K/AKT Signaling 63 0.048 0.197 RAF1, MAPK1, INPPL1, KRAS, JAK2, MAP3K5, EIF4E, PTEN, BCL2, SHC1, IKBKG, SOS1, TSC2, GSK3B, MCL1, ITGB1, RPS6KB1, YWHAG, PPP2R5C, ITGA2, TYK2, YWHAZ, PPP2R5A, PPP2CB, GAB1, CDKN1B, PPP2R5E, PPP2R1B
91 0.296 0.021 PTGS2, PPP2R5A, BCL2
α-Adrenergic Signaling 63 0.012 0.236 PRKACB, RAF1, MAPK1, GNB5, KRAS, PRKAG1, PHKA2, GNB1, GNB4, PHKB, PRKD3, PRKCA, null, ITPR2, GNAI1, ADCY6, GNAQ, GNAS, GNAI3, PRKCI, PRKAR2B, PRKAG2, PRKCH, GNG2, PRKCB
91 0.404 0.019 PRKAR2B, ADCY3
IL-15 Signaling 63 0.047 0.229 STAT5A, RAF1, PIK3C2A, MAPK1, TYK2, KRAS, JAK2, AXL, MAPK12, PIK3R4, BCL2, SHC1, MAPK14, PIK3C3, SYK, ATM
91 0.267 0.029 STAT6, BCL2
Myc Mediated Apoptosis Signaling 63 0.018 0.266 MAP2K4, YWHAG, PIK3C2A, MAPK8, YWHAZ, MAPK9, KRAS, PIK3R4, MAPK12, BCL2, SHC1, IGF1, PIK3C3, SOS1, CYCS, BID, ATM
91 0.255 0.031 APAF1, BCL2
Protein Kinase A Signaling 63 0.000 0.228 PRKACB, MYH10, RAF1, TGFBR1, MAPK1, MYL2, PDE12, GNB5, AKAP3, CREB5, PPP1R14B, TGFBR2, GNB1, GNB4, PHKB, CAMK2A, TDP2, GSK3B, PRKD3, null, YWHAG, ITPR2, PTCH1, CREBBP, YWHAZ, RAP1A, MYL6B, TTN, ATF2, MYL9, AKAP13, ANAPC4, ANAPC5, PPP1R12A, PRKCH, LEF1, GNG2, PDE6D, AKAP12, RAP1B, PPP1CC, FLNB, PDE7A, AKAP8, PDIA3, PPP1CB, H3F3A/H3F3B, CDC23, PRKAG1, PHKA2, NFAT5, TGFB2, SMAD4, PPP3CA, PRKCA, AKAP5, ATF1, MAP3K1, ADCY6, GNAI1, GNAQ, ANAPC13, ROCK1, GNAS, GNAI3, PPP1R3D, PRKAR2B, PRKCI, ADD3, KDELR2, PRKAG2, AKAP9, PRKCB, ANAPC1
91 0.348 0.019 ADD3, PRKAR2B, ADCY3, AKAP3, AKAP7, TTN
Molecular Mechanisms of Cancer 63 0.000 0.275 RAP2B,RAF1,TGFBR1,APH1B,TAB2,ARHGEF1,KRAS,RBL1,RB1,CAMK2A,HIPK2,PRKD3,ATM,SMAD2,TFDP1,PTCH1,CREBBP,RAP1A,CDH1,GAB1,E2F1,CYCS,CFLAR,RAP1B,FYN,RALA,CDC42,LRP6,BMPR2,CRK,JAK2,MAP3K5,GNA14,CHEK1,CASP6,PIK3C3,SOS1,E2F5,BID,BMP1,PAK2,GNAQ,ADCY6,MAPK8,GNAI3,RBPJ,ATR,BIRC2,PSEN1,PRKCB,MAP2K4,PRKACB,MAPK1,PIK3R4,TGFBR2,RHOG,GSK3B,RASA1,BIRC3,TYK2,CDK6,MAPK12,RALBP1,APC,RHOQ,CBL,PTPN11,RND3,FZD6,PRKCH,LEF1,FZD5,CDK2,HIF1A,E2F3,PRKAG1,BCL2,CDC25B,SHC1,FANCD2,RHOT1,BMPR1A,MAP3K7,TGFB2,SMAD4,PRKCA,ARHGEF12,PIK3C2A,HAT1,GNAI1,MAPK9,XIAP,GNAS,PRKCI,MAPK14,PRKAR2B,FZD4,NF1,BMP8B,PRKAG2,CDKN1B,GLI1,BCL2L11
91 0.017 0.029 PRKAR2B,RALA,FZD4,ADCY3,APAF1,RAPGEF3,E2F3,CASP7,E2F2,WNT5A,BCL2
p53 Signaling 63 0.000 0.293 GADD45G, PIK3R4, PTEN, CHEK1, BCL2, RB1, CASP6, GADD45A, PIK3C3, GSK3B, HIPK2, ATM, TP53INP1, TP63, PIK3C2A, TOPBP1, MED1, THBS1, HDAC1, PERP, MAPK8, TP53BP2, KAT2B, PCNA, MAPK14, E2F1, ATR, CDK2, SIRT1
91 0.192 0.030 MED1, APAF1, BCL2
VDR/RXR Activation 63 0.003 0.284 CYP24A1, SPP1, CCNC, MED1, IGFBP5, CEBPB, THBD, KLF4, NCOA3, GTF2B, PRKCI, SP1, GADD45A, NCOA2, MXD1, NCOA1, IGFBP3, TGFB2, PRKCH, CDKN1B, PRKD3, PRKCA, PRKCB
91 0.124 0.037 CYP24A1, MED1, MXD1
Breast Cancer Regulation by Stathmin1 63 0.000 0.248 PRKACB, RAF1, CAMK1D, MAPK1, GNB5, KRAS, ARHGEF1, PIK3R4, PPP1R14B, GNB1, GNB4, CAMK2A, PRKD3, ATM, null, ITPR2, PPP2CB, E2F1, PPP1R12A, PRKCH, GNG2, CDK2, PPP1CC, CDC42, PPP1CB, E2F3, PRKAG1, SHC1, PIK3C3, SOS1, RB1CC1, E2F5, PRKCA, ARHGEF12, PIK3C2A, PPP2R5C, GNAI1, TUBA4A, ADCY6, GNAQ, PPP2R5A, ROCK1, GNAS, GNAI3, PPP1R3D, PRKCI, PRKAR2B, PRKAG2, CDKN1B, PPP2R5E, PPP2R1B, PRKCB
91 0.191 0.024 PRKAR2B, ADCY3, E2F3, E2F2, PPP2R5A
ERK/MAPK Signaling 63 0.001 0.230 RAP1B, PRKACB, FYN, PPP1CC, RAF1, MAPK1, HSPB2, H3F3A/H3F3B, ETS2, PPP1CB, KRAS, CRK, PIK3R4, CREB5, PPP1R14B, EIF4E, PRKAG1, SHC1, PIK3C3, SOS1, MKNK1, PRKCA, ATM, ITGB1, MYCN, PAK2, YWHAG, PPP2R5C, ATF1, PIK3C2A, ITGA2, YWHAZ, MAPKAPK5, RAP1A, PPP2R5A, ATF2, PLA2G4A, PPP2CB, PPP1R3D, PRKCI, PRKAR2B, PRKAG2, PPP1R12A, PPP2R5E, PPP2R1B, ELK3, PRKCB
91 0.556 0.015 PRKAR2B, RAPGEF3, PPP2R5A
RAR Activation 63 0.001 0.246 MAP2K4, PRKACB, NSD1, MAPK1, MAP3K5, JAK2,RBP1, PRKAG1, PTEN, PNRC1, TGFB2, SMAD4, GTF2H5, NR2F6, RDH13, PRKD3, CITED2, PRKCA, STAT5A, SMAD2, SRA1, PRMT2, IL3RA, RDH14, MED1, RDH11, MAP3K1, CREBBP, MAPK8, ADCY6, MAPK9, MAPK12, CRABP1, PARP1, KAT2B, PRKCI, MAPK14, PRKAR2B, TAF4, ERCC3, IGFBP3, NCOA1, PRKAG2, PRKCH, PRKCB
  91 0.269 0.022 PRKAR2B, MED1, ADCY3, RDH13
  1. 1pathways are shown that were significant at p < 0.05 according to Fishers exact test in at minimum one of the three types of comparisons.
  2. 2ratio of number of differentially expression genes assigned to the pathway and the total number of genes assigned to the pathway in the Ingenuity Knowledge Base.
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BMC Developmental Biology

ISSN: 1471-213X

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