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 1 Assignment of temporally regulated DE-genes to canonical pathways in German Landrace and Pietrain, respectively

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	63 dpc vs. 91 dpc in GL or PI	p-value¹	Ratio²	Molecules
Angiopoietin Signaling	GL	0.008	0.143	STAT5A, PAK4, AKT2, IKBKG, TNIP1, GRB14, ANGPT1, PAK6, PTPN11, MRAS, IKBKAP
Angiopoietin Signaling	PI	0.065	0.065	PIK3C2B, PAK4, IKBKG, TNIP1, PIK3R4
Chemokine Signaling	GL	0.028	0.133	GNAI3, PLCB4, JUN, MYL2, CXCL12, MRAS, GNAQ, PPP1R12A, MAPK12, CAMK2G
Chemokine Signaling	PI	0.393	0.040	CAMK2A, MYL2, CAMK2G
ILK Signaling	GL	0.005	0.120	MYH10, AKT2, VEGFB, MYL2, TNFRSF1A, CREB3, MYH11, MAPK12, MYL9, NCK2, RHOQ, JUN, RHOG, IRS1, RHOU, CHD1, MYH9, LEF1, ACTG2, PTGS2, PPP2R5E, ACTC1, ACTN1
ILK Signaling	PI	0.002	0.073	PIK3C2B, MYL2, TNFRSF1A, VEGFC, MYH11, PIK3R4, MYL6B, PPP2R5A, ITGB3, PPP2R4, PPP2R2B, MYH3, PTGS2, ACTC1
Integrin Signaling	GL	0.011	0.112	CAPN5, FYN, AKT2, PAK4, ARHGAP26, TSPAN7, MYL2, PAK6, ARHGEF7, TNK2, MYLK, NCK2, RHOG, RHOQ, MRAS, RHOU, PPP1R12A, ITGA1, ACTG2, ACTC1, ACTN1, RAP2A, RAPGEF1
Integrin Signaling	PI	0.275	0.039	PIK3C2B, PAK4, MYL2, TSPAN7, PIK3R4, ACTC1, TTN, ITGB3
TGF-β Signaling	GL	0.008	0.145	SMAD2, BMPR1B, JUN, SMAD9, TGFB1, MRAS, TGFB3, TGFB2, SMAD6, PITX2, SMAD1, INHBB
TGF-β Signaling	PI	0.228	0.048	SMAD2, TGFB1, TGFB3, INHBB
Wnt/β-catenin Signaling	GL	0.019	0.114	AKT2, SFRP2, APPL2, PPARD, WNT2B, MARK2, GNAQ, APPL1, CDH2, JUN, TGFB1, CSNK2A1, TGFB2, TGFB3, NR5A2, FZD5, LEF1, SFRP1, PPP2R5E, TCF7L2
Wnt/β-catenin Signaling	PI	0.046	0.057	CDH2, CDH1, PPP2R4, TGFB1, PPP2R2B, CD44, TGFB3, FZD6, TLE1, PPP2R5A
Cyclins and Cell Cycle Regulation	GL	0.023	0.124	CCND3, PA2G4, HDAC8, TGFB1, E2F1, HDAC7, E2F5, TGFB3, TGFB2, PPP2R5E, SKP2
Cyclins and Cell Cycle Regulation	PI	0.003	0.090	CCNE2, PPP2R4, TGFB1, PPP2R2B, TGFB3, CCNB2, ATR, PPP2R5A
Aryl Hydrocarbon Receptor Signaling	GL	0.007	0.116	ALDH4A1, NFIC, MED1, HSPB2, CYP1B1, CTSD, ALDH1A1, JUN, CCND3, NCOA2, TGFB1, E2F1, TGFB3, TGFB2, IL1B, NFIB, NCOR2, ESR1
Aryl Hydrocarbon Receptor Signaling	PI	0.004	0.071	ALDH4A1, CCNE2, ALDH1A1, TGFB1, TGFB3, IL1B, ALDH18A1, NCOR2, ATR, ESR1, NCOA3
Gα12/13 Signaling	GL	0.043	0.109	F2RL2, AKT2, F2R, MYL2, MAPK12, LPAR3, CDH11, MYL9, CDH2, IKBKG, JUN, LPAR1, MRAS, MAPK7
Gα12/13 Signaling	PI	0.005	0.078	PIK3C2B, CDH2, CDH1, IKBKG, MYL2, MEF2C, MAP3K5, MAPK7, PIK3R4, MYL6B
Glucocorticoid Receptor Signaling	GL	0.025	0.095	ICAM1, GTF2A2, TSC22D3, IKBKG, JUN, NCOA2, TGFB1, MRAS, TGFB2, GTF2H5, POLR2H, NCOR1, FKBP5, TAF12, SMAD2, STAT5A, AKT2, MED1, TAF15, CEBPB, MAPK12, NCOA1, TGFB3, IL1B, PTGS2, NCOR2,ESR1
Glucocorticoid Receptor Signaling	PI	0.033	0.049	SMAD2, PIK3C2B, SMARCD2, CEBPB, PIK3R4, NCOA3, TSC22D3, IKBKG, TGFB1, TGFB3, IL1B, NCOR2, PTGS2, ESR1
Ceramide Signaling	GL	0.352	0.078	CTSD, AKT2, JUN, TNFRSF1A, MRAS, PPP2R5E, TNFRSF1B
Ceramide Signaling	PI	0.044	0.067	PIK3C2B, PPP2R4, TNFRSF1A, PPP2R2B, PIK3R4, PPP2R5A
PPARα/RXRα Activation	GL	0.002	0.123	PPARA, SMAD2, MED1, ADCY3, GNAQ, ADCY6, MAP4K4, CAND1, PLCD1, PLCD3, IKBKG, PLCB4, JUN, TGFB1, FASN, IRS1, MRAS, TGFB3, TGFB2, IL1B, NCOR1, NCOR2, INSR
PPARα/RXRα Activation	PI	0.020	0.059	PLCD1, SMAD2, IKBKG, TGFB1, GNA11, ADCY6, TGFB3, IL1B, NCOR2, NCOA3, ABCA1
RhoA Signaling	GL	0.019	0.127	MYL2, RDX, WASF1, DLC1, LPAR3, MYLK, MYL9, LPAR1, IGF1R, PPP1R12A, CDC42EP1, ACTG2, ACTC1, PI4KA
RhoA Signaling	PI	0.007	0.082	RHPN2, IGF1, MYL2, EPHA1, IGF1R, ARHGAP12, MYL6B, ACTC1, TTN
Tight Junction Signaling	GL	0.004	0.127	MYH10, F2RL2, TIAM1, AKT2, MYL2, TNFRSF1A, PVRL3, MARK2, MYH11, CASK, MYL9, MYLK, JUN, TGFB1, TGFB3, TGFB2, MYH9, ACTG2, PPP2R5E, TNFRSF1B, ACTC1
Tight Junction Signaling	PI	0.005	0.072	MYL2, CLDN8, PPP2R4, TGFB1, TNFRSF1A, PPP2R2B, MYH3, TGFB3, MYH11, MYL6B, ACTC1, PPP2R5A
Estrogen-Dependent Breast Cancer Signaling	GL	0.076	0.110	STAT5A, AKT2, JUN, CREB3, IGF1R, MRAS, HSD17B7, ESR1
Estrogen-Dependent Breast Cancer Signaling	PI	0.014	0.082	PIK3C2B, IGF1, IGF1R, PIK3R4, ESR1, HSD17B8
Mitotic Roles of Polo-Like Kinase	GL	0.424	0.079	CDC25B, TGFB1, CDC23, PPP2R5E, ANAPC13
Mitotic Roles of Polo-Like Kinase	PI	0.012	0.095	PPP2R4, TGFB1, PPP2R2B, CCNB2, CDC27, PPP2R5A
PPAR Signaling	GL	0.000	0.170	PPARA, STAT5A, TNFRSF1A, PPARD, MED1, MAP4K4, IKBKG, JUN, NCOA1, MRAS, IL1B, NCOR1, PTGS2, NCOR2, INSR, TNFRSF1B, CITED2, PDGFRB
PPAR Signaling	PI	0.081	0.057	IKBKG, TNFRSF1A, IL1B, NCOR2, PTGS2, PDGFRB
Role of Tissue Factor in Cancer	GL	0.164	0.095	FYN, STAT5A, YES1, AKT2, PTPN11, MRAS, GNAQ, IL1B, GNA14, RPS6KA1, MAPK12
Role of Tissue Factor in Cancer	PI	0.009	0.078	PIK3C2B, CTGF, CSF1, GNA11, VEGFC, IL1B, RPS6KA1, PIK3R4, ITGB3
TR/RXR Activation	GL	0.010	0.130	AKT2, NXPH2, MED1, THRA, KLF9, SCARB1, COL6A3, NCOA2, FASN, NCOA1, STRBP, NCOR1, NCOR2
	PI	0.063	0.060	KLF9, PIK3C2B, COL6A3, NCOR2, PIK3R4, NCOA3

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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ISSN: 1471-213X

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