Table 4.

GO biological process representative of top ten overrepresented functional annotation clusters among genes overexpressed in embryos versus somatic cells at P < 0.001 and 10 FC

Biological process	Gene count	P value	Genes
Chordate embryonic development	27	4.6E-6	HNF1B, CDX2, PTK7, CITED1, ZIC2, GATA2, DAB2, POU5F1, RSPO3, TDGF1, KRT8, HOXC5, AXIN2, GINS1, GSC, TBX3, ESRRB, NASP, GJB5, SLC34A2, CCNB1, HOXB4, GCM1, SALL4, PDGFRA, HOXB9, MYH10
Blastocyst development	6	0.007	GINS1, HNF1B, CDX2, ESRRB, POU5F1, NASP
Pattern specification process	16	0.002	NANOG, HNF1B, GSC, CDX2, TBX3, OTX2, ZIC3, TCF7L1, HOXB4, LHX2, FOXG1, HOXC5, TDGF1, HOXB9, HHIP, AXIN2
Negative regulation of gene expression	21	0.001	DNMT3A, NANOG, GSC, CDX2, TBX3, RCOR2, SOX2, MLXIPL, MAEL, CENPF, TNP1, LIN28A, PKIA, LIN28B, TCF7L1, HOXB4, SALL4, POU5F1, SOX15, DNMT3B, TDRD1
Placenta development	9	8.5E-4	GATA2, CDX2, GCM1, ESRRB, RSPO3, KRT8, GJB3, GJB5, CITED1
Cellular component morphogenesis	23	2.1E-5	CCDC99, ACTC1, NDN, ESRRB, PDPN, MYBPC3, KIF5C, PTK7, MAEL, SLITRK2, LAMA1, DAB2, BDNF, LAMB2, PRDM14, FAT1, LHX2, FOXG1, KRT8, SLITRK5, NEFL, MYH10, GFRA3
Stem cell maintenance	5	0.001	NANOG, CDX2, ESRRB, POU5F1, SOX2
Cell adhesion	24	0.005	TYRO3, CADM3, MPZL2, ATP1B2, CLSTN3, PDPN, CLDN6, MYBPC3, FERMT2, PTK7, BCAM, AMIGO2, LAMA1, LAMB2, DSG2, SORBS1, DSG3, PKP2, FAT1, FREM1, PECAM1, COL12A1, CNTNAP1, ESAM
Establishment of organelle localization	5	0.007	CCDC99, NPM1, CENPF, CDCA5, MYH10
Regulation of glucose metabolic process	4	0.003	HNF4A, SORBS1, MLXIPL, GNMT