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

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