Table 1. Top 10 networks generated using IPA for the “reprogrammed transcriptome in rhesus/bovine iSCNT (R/B iSCNT) 8- to 16- cell embryos.”.

ID	IPA Score	No. of Focus Molecules	Molecules in Top Network	Top Functions
1	43	33	ABTB2, ADNP, C22ORF28, CCR6, CD6, CX3CR1, EEA1, ELAVL2, GDI2, GM2A, GNL1, GPD2, ICEBERG, ICOSLG, IER2, KPNA3, M6PRBP1, MUC5AC, NR6A1, NUP50, OGN, PLP1, PRKAA, Rab5, RAB14, RAB5C, SCUBE1, SEPP1, STAP2, SUPT4H1, TNF, TNFRSF21, TUB, WTAP, ZBTB11	Cellular Development, Cellular Growth and Proliferation, Hematological System Development and Function
2	41	32	AKT2, Alcohol group acceptor phosphotransferase, BAT5, CCR5, CDK6, CSK, Cytochrome c, FOXC1, FZR1, G3BP1, GMNN, GRK6, HIPK3, HM13, HOXA7, HOXB6 (includes EG:3216), HOXD10, Integrin, MAK, MAPK8, MBD1, MBD3 (includes EG:53615), NEDD9, NEUROD1, PAX6, PBX1, POU2F2, PRKAA1, PRKAA2, PRKCE, PTPN18, RREB1, RSBN1, SOX3, TOX4	Organismal Development, Cancer, Reproductive System Disease
3	41	32	ALP, BCL2L1, BMP2, BRPF1, CBX3, CCNE1, CGGBP1, CHRDL2, CXORF15, E2f, EIF3A, FMR1, GBX2, GOLM1, GRIK5, HIST1H1E, HIST1H3B (includes EG:8358), MYB, NOTCH1, PAX9, PMP22, POU4F2, PRR11, RAG2, RGS32, RORA, SHH, SKP2, SND1, Stat3-Stat3, TCF3, TCF21, TFE3, ZFAND3, ZP1	Cellular Growth and Proliferation, Cell Morphology, Hematological System Development and Function
4	41	32	ANAPC1, ARS2, ASXL2, BRD8, CLDND1, CROP, Cyclin B, ELL2, EZH2, GEMIN4, GTF3C1, Histone h3, ING3, KAT5, KIAA0265, KIAA1310, KPNA4, MED31, MNDA, MYBBP1A, NFE2, NOC2L, PBX3, PIN4, PNN, PRPF19, PRUNE, RBM33, RNA polymerase II, RRP1, SETMAR, TCEA1, TMPO, XIST, ZNF143	Gene Expression, DNA Replication, Recombination, and Repair, Cell-To-Cell Signaling and Interaction
5	38	31	AIFM2, ANKH, ARPC1B, C14ORF106, CADM1, CDC14B, CITED1, CNOT4, Creatine Kinase, GADD45, GIGYF2, GTSE1, Jnk dimer, NBR1, PRKAB2, PSRC1, PVRL1, PVRL3, RBBP6 (includes EG:5930), RRN3, SMA4, SNRK, SNRPN, STAG1, STK17A, TAF1A, TP53, UBA6, UBE2, UBE2D2, UBE2E1, UBE2E3, UBE3A, WAPAL, ZNF84	Developmental Disorder, Ophthalmic Disease, Cancer
6	36	30	ACY1, APAF1, BAG4, Caspase, CFLAR, CYCS (includes EG:54205), DEDD, DPPA2, DPPA4, FEM1B, Hsp70, Hsp90, HSPA6, HSPBP1, KHDC1, NLRP1, NLRP3, NOD1, NR3C2, OSBPL2, PDGF BB, PRPF4, RIPK2, RPS14, RYBP, SFRS1, SFRS7, SFRS10, Sphk, SRPK1, TNFAIP3, TRA2A, TRIOBP, U2AF2 (includes EG:11338), ZNF250	RNA Posttranscriptional Modification, Cell Death, Cancer
7	32	28	CR2, DLK1, ERK, F11R, Fgf, FGF4, FGF9, FGF10, Fgfr, FGFR1, FGFR2, FRS2, GPR132, IL17RD, LAMA3, Mmp, MMP7, MMP11, MMP28, NGEF, NODAL, NTRK2, Opsin, PCSK7, PLC gamma, RABGEF1, RAPGEF2, SAG, SERPINA1, SLC35E1, SLC9A3, SPZ1, Tgf beta, TGFA, ZNF384	Cellular Growth and Proliferation, Embryonic Development, Tissue Development
8	32	28	ARF6, ATF7IP, ATPase, BAT1, C2ORF13, CFD, Ck2, CSNK2B, CTSB, DDX19B, DHX8, FCGR1A/2A/3A, GGA1, KIAA1632, KRT13, KRT6B, MAX, MGA (includes EG:23269), MYH9, Myosin, Myosin Light Chain Kinase, NKX3-1, NPEPPS, PEX6, PIP5K1A, PTK2B, RAD51C, SENP3, SRPRB, STARD10, STXBP1, Tni, TRIM63, Tubulin, XPO7	Gene Expression, Molecular Transport, RNA Trafficking
9	30	27	ALDH7A1, ALS2CR2, AMH, BCL2L2, Bmpr1, BMPR1A, Caspase 3/7, CDH22, CHRNA3, CHRNA9, COMMD1 (includes EG:150684), CRIM2, FGG, HLA-F, IL1F6, Jnkk, Map3k, MAP3K2, MAP3K3, MEKK, MTSS1, NAIP, NF-κB, NFkB, Nicotinic acetylcholine receptor, OLR1, PLK3, PTPRD, SNIP1, ST8SIA1, TAP2, WNK1, XIAP, ZAK, ZNF33A	Amino Acid Metabolism, Posttranslational Modification, Small Molecule Biochemistry
10	30	27	BNIP3L, CAMTA1, CD3, CD8, CD247, CD8A, CLCA2 (includes EG:9635), CNOT1, CNOT2, CNOT6L, ERN1 (includes EG:2081), GAB3, GCN1L1, GRAP2, IL18R1, IL18RAP, LAT, LDB3, MAPK8IP2, MEF2, MHC Class I, MYH3, NFAT complex, NFATC1, P38 MAPK, PTPRC, RINT1, SCN5A, SLC9A8, SOS2, SYK/ZAP, TAOK2 (includes EG:9344), TCR, TRA@, TRIM27	Gene Expression, Hematological System Development and Function, Immune and Lymphatic System Development and Function

IPA score = −(log (P value)); IPA score is associated with the significance of the selected gene network. The higher the score, the more chance that it is true (from IPA).