Table 3. Process network enrichment in MetaCore.

Category	Process Network	Genes	P value	FDR
Signal Transduction	TGF-β, GDF and Activin signaling	PTPRK, PTGER2, CREB1, GATA3, CCND1, INHBA, SMAD4, FOS, SP1, SMAD2, HIF1A, ATF2, SMAD7, LEFTY1, MYC, TOB1, NOTCH1, CDK6	3.54E-04	0.044*
Signal Transduction	BMP and GDF signaling	CREB1, MSX2, BMPR1A, AKT1, BMP7, SMAD4, TLE1, ATF2, SMAD7, MYC, NODAL, SOX9, TOB1, CDK6	8.02E-04	0.044*
Development	Regulation of epithelial-to-mesenchymal transition	NOTCH1, CREB1, ACTA2, JAK2, BMP7, TRADD, SMAD4, FOS, SP1, SMAD2, HIF1A, ATF2, ABBP1, JAG1, SMAD7, ADAM17, SNAI2, IGF2, TJP1, SOX9	8.38E-04	0.044*
Development	Regulation of telomere length	TINF2, MAX, TEP1, SP1, HNRNPC, MYC, PTGES3, CDK6	5.35E-03	0.190
Development	Hedgehog signaling	NOTCH1, CREB1, HESX1, CCND1, SIRT1, INHBA, AKT1, BMP7, RBX1, SMAD4, ASCL1, ZIC1, SP1, ROCK2, PBX1. CDKN1C, HES1, JAG1, MYC, ADAM17, SOX9	6.06E-03	0.190
Apoptosis	Death Domain receptors and caspases in apoptosis	NGFRAP1, NGFR, TRADD, CD40, TIMP3, TNFSF10, CASP1, TRAF4, NOD1, PDCD5, CASP3, BIRC8, FAS, CASP4, CARD8	7.26E-03	0.190
Apoptosis	Apoptosis stimulation by external signals	NGFRAP1, JAK2, BID, NGFR, NTRK1, TRADD, SMAD4, TNFSF10, FOS, SMAD2, ADAM17, CASP3, FAS, BID	9.66E-03	0.217
Development	Neurogenesis in general	NOTCH1, CREB1, HESX1, GFRA3, INHBA, RCAN1, ASCL1, ZIC1, PBX1, NEUROG2, HES1, JAG1, ADAM17, CHRM3, MEF2C, SERPINI1	1.24E-02	0.237
DNA damage	Checkpoint	YWHAQ, CCND1, TLK2, BRIP1, CCND3, RUVBL2, ATF2, ATF3, RAD1, BARD1, MYC, YWHAZ, CDK6	1.51E-02	0.237
Cardiac development	BMP and TGF-β signaling	MSX2, ISL1, BMPR1A, BMP7, SMAD4, PDLIM3, MYH7, SMAD2, SMAD7, NODAL, SNAI2, SOX9, MEF2C	1.51E-02	0.237

The Entrez gene IDs derived from the high-confidence list of 1031 differentially expressed genes in TCF4-knockdown cells were analyzed for enrichment using MetaCore^TM. Each term is presented with its functional category, network and corresponding P value. * Pass FDR correction of 0.05.