Table 1.

Gene sets associated with human ES cell identity.

Group	Gene Set	No. of Genes	Source	Reference
ES expressed	ES exp1	380	Overexpressed in hES cells according to 5 or more out of 20 profiling studies	Assou et al. 2006
	ES exp2	40	Overexpressed in hES cells according to a meta-analysis of 8 profiling studies	Assou et al. 2006
NOS targets	Nanog targets	988	ChIP-array of Nanog in hES cells, activated genes only	Boyer et al. 2005
	Oct4 targets	290	ChIP-array of Oct4 in hES cells, activated genes only	Boyer et al. 2005
	Sox2 targets	734	ChIP-array of Sox2 in hES cells, activated genes only	Boyer et al. 2005
	NOS targets	179	Overlap of above three sets	Boyer et al. 2005
	NOS TFs	37	Transcription regulators in NOS targets set
Polycomb targets	Suz12 targets	1040	ChIP-array of Suz12 in hES cells	Lee et al. 2006
	Eed targets	1066	ChIP-array of Eed in hES cells	Lee et al. 2006
	H3K27 bound	1121	ChIP-array of trimethlyated H3K27 in hES cells	Lee et al. 2006
	PRC2 targets	654	Overlap of 3 above sets	Lee et al. 2006
Myc targets	Myc targets1	230	ChIP array of c-Myc in cultured cell lines, focusing on E-box containing genes - high affinity bound subset.	Fernandez et al. 2003
	Myc targets2	775	ChIP array of c-Myc and of Max in a Bukitt’s Lymphoma cell line, overlap set.	Li et al. 2003