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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
  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.