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 |