Table 1. Boolean definition for genes in the model
GeneGene categoryBoolean definition
Activin A/NodalCytokine(SignalACT or Oct4) and (not Sox2) and (not Lefty1) and (not Gbx2)
BMP4CytokineSignalBMP or Gbx2 or Tbx3 or Myc
Dnmt3bEnzyme(Mycn or Tcf3 or EpiTFs) and not (Cdx2 or Klf4)
EpiTFsLineage TF(SignalBMP or Pitx2 or Dusp6) and (not Cdx2) and not (Klf4 and Sox2)
EsrrbPluripotency TF(Klf4 or Klf2 or Nanog or (SignalWNT and (not Tcf3))) and (not EpiTFs)
Fgfr2Receptor((SignalFGF) or Gcnf or Cdx2) and (not Nanog) and (not Oct4)
Gata6Lineage TF(Gata6 or SignalERK) and (not Klf2) and (not Nanog) and (not Fgf4)
Gbx2Pluripotency TF((SignalWNT and (not Tcf3)) or SignalLIF) and ((Esrrb or Jarid2) and not (Tbx3))
GcnfLineage TF(Gata6 or Cdx2) and (not EpiTFs)
Jarid2Pluripotency TFKlf4 or Oct4
Klf4Pluripotency TF(SignalLIF or ((Klf2 or Klf4) and Nanog and Esrrb and (Oct4 and Sox2))) and (not EpiTFs)
NanogPluripotency TF(Nanog or SignalACT or (Oct4 and Sox2) or Tbx3 or Lrh1 or Klf4) and not (Tcf3 or Gata6)
Oct4Pluripotency TF(((Oct4 and Sox2) or Nanog or Klf2 or Klf4) and not (Cdx2 and Oct4) and (not Dnmt3b or Klf2)) or (((Oct4 and Sox2) or Nanog or Lrh1 or Klf2 or Klf4) and (not Gcnf) and (Dnmt3b and (not Klf2)))
Smad6Signal antagonist(SignalBMP or Gata6) and (not Oct4)
Smad7Signal antagonist(Oct4 or Nanog or Esrrb or Klf4 or Tbx3) and (not Gbx2) and (not Jarid2)
Sox2Pluripotency TFNanog or (Oct4 and Sox2)
Tcf3Lineage TF(Nanog or Oct4) and (not SignalWNT)
Cdx2Lineage TF(SignalBMP or Cdx2) and not (Cdx2 and Oct4)
Dusp6TFSignalERK
Fgf4Pluripotency TF/CytokineEsrrb or Nanog or (SignalWNT and (not Tcf3))
Klf2Pluripotency TF((Sox2 and Klf4) or Mycn) and (not Pitx2) and (not Dusp6)
Lefty1TF(SignalACT or (SignalWNT(not Tcf3))) or Mycn or (Oct4 and Sox2)) and (not Jarid2) and (not Fgf4)
Lrh1Pluripotency TF(Tbx3 or Klf4 or (Oct4 and Sox2)) and (not Tcf3)
MycnTF(Oct4 and Sox2) and (not Nanog)
Pitx2TF(SignalACT or (SignalWNT(not Tcf3))) and (not Sox2) and (not Jarid2)
Tbx3Pluripotency TF(SignalPI3K or Tbx3) and (Esrrb or Nanog or Klf4) and (not SignalERK) and (not Tcf3)
MycPluripotency TF((SignalERK or (SignalWNT and (not Tcf3))) or SignalLIF or Gbx2) and (not Nanog)
Pecam1Pluripotency Marker(Klf2 or Nanog) and (not EpiTFs)
Rex1Pluripotency Marker(Nanog or Sox2 or Lrh1 or Klf2 or Esrrb) and (not EpiTFs)