TABLE I.

GREAT (Genomic Region Element Annotation Tool) Ontological analysis of genes associated with FAIRE

Cell line	All ESC clusters	All EpiSC clusters	ESC-specific clusters	EpiSC- specific clusters	ESC/EpiSC shared Clusters
Biological Process	negative regulation of gene expression 0	embryo development 7.6E-278	protein complex subunit organization 2.9E-134	embryonic morphogenesis 1.1E-64	regulation of cellular metabolic process 2.7E-285
	chordate embryonic development 3.6E-319	negative regulation of gene expression 2.E-229	in utero embryonic development 1.5E-132	pattern specification process 4.20E-62	regulation of macromolecule metabolic process 2.1E-272
	in utero embryonic development 8.3E-213	embryonic morphogenesis 2.4E-191	posttranscriptional regulation of gene expression 1.7E-105	regionalization 3.6E-54	regulation of gene expression 3.7E-239
Mouse Phenotype	prenatal lethality 0	abnormal embryonic tissue morphology 5.2E-287	prenatal growth retardation 2E-224	abnormal neuron differentiation 10E-45	prenatal lethality 6.5E-155
	embryonic lethality 0	embryonic lethality during organogenesis 1.1E-253	decreased embryo size 1.04E-215	partial neonatal lethality 5.8E-40	abnormal embryogenesis/ development 1.9E-143
	embryonic lethality between implantation and placentation 0	abnormal neural tube closure 7.8E-129	abnormal placenta morphology 1.85E-146	abnormal nervous system tract 7.1E-38	abnormal nervous system development 8.8E-117
Expression	TS4 inner cell mass 0	TS21_embryo; head 1.2E-283	TS4_inner cell mass 0	TS17_brain 2.4E-91	TS17_embryo 2E-298
	TS4 extraembryonic component 0	TS17_limb 5.59E-272	TS4_extraembryonic component 0	TS15_embryo; mesenchyme 3.3E-63	Theiler_stage_19 1.1E-254
	Theiler stage 3 0	TS3_4–8 cell stage 1.3E-253	Theiler stage 3 0	TS12_embryo 1.7E-57	TS23_metanephros 3.9E-240
Perturbation	Genes up-regulated in CD34+ cells isolated from bone marrow of CML 0	Genes with copy number losses in primary neuroblastoma tumors. 5.2E-204	Genes constituting the BRCA1-PCC network 0	'PRC2 targets': trimethylated H3K27 mark in their promoters and are bound by SUZ12 and EED 7.9E-86	'H3K27 bound': genes possessing the H3K27me3 mark in their promoters in human embryonic stem cells 8.5E-126
	Set 'Nanog targets': genes in human embryonic stem cells. 0	Housekeeping genes identified as expressed across 19 normal tissues. 1.4E-120	Genes down-regulated in prostate cancer after knockdown of NIPP1 0	Genes with copy number gains in primary neuroblastoma tumors. 3.9E-26	Eed target genes in human embryonic stem cells 2.2E-106
	Set 'Sox2 targets': genes in human embryonic stem cells 0	Genes up-regulated in lymphoblastoid cells 7.2E-105	Set 'Sox2 targets': genes in human embryonic stem cells 7.2E-268	Genes bearing H3K27me3 mark or bound by SUZ12 or EED 4.8E-19	'PRC2 targets': trimethylated H3K27 mark in their promoters and are bound by SUZ12 and EED 4E-97