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

Chomwisarutkun, Kunsuda; Murani, Eduard; Ponsuksili, Siriluck; Wimmers, Klaus

doi:10.1186/1471-213X-12-13

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
Clathrin-mediated Endocytosis Signaling	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
Corticotropin Releasing Hormone Signaling	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
Integrin Signaling	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
PI3K/AKT Signaling	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
α-Adrenergic Signaling	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
IL-15 Signaling	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
Myc Mediated Apoptosis Signaling	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
Protein Kinase A Signaling	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
Molecular Mechanisms of Cancer	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
p53 Signaling	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
VDR/RXR Activation	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
Breast Cancer Regulation by Stathmin1	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
ERK/MAPK Signaling	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

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.
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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