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Table 1 hESC-associated gene sets

From: Computational analysis of expression of human embryonic stem cell-associated signatures in tumors

Group

Gene set

#Genes

Description

 

hESC exp1

379

Overexpressed in hESCs according to 5 or more out of 20 profiling studies

 

hESC exp2

40

Overexpressed in hESCs according to a meta-analysis of 8 profiling studies

 

hESC exp3

48

Overexpressed in hESCs in at least 10 studies

 

hESC exp4

30

Underexpressed in hESCs in at least 6 studies

 

hESC exp5

189

TF genes in hESCs

hESC expressed

hESC exp6

44

Highly expressed in undifferentiated hESCs

 

hESC exp7

994

High connectivity (≥ 500) in the global co-expression networks of hESCs

 

hESC exp8

22

Candidate hESC markers

 

hESC exp9

27

Differentially upregulated in hESCs

 

hESC exp10

31

The most abundant transcripts expressed in hESCs

 

hESC exp11

1, 000

Significantly identified in hESC lines by SAM analysis

 

Nanog targets

988

Genes activated by Nanog in hESCs

 

Oct4 targets

290

Genes activated by Oct4 in hESCs

NOS targets

Sox2 targets

734

Genes activated by Sox2 in hESCs

 

NOS targets

179

Overlap of three above sets

 

NOS TFs

37

Transcription regulators in NOS targets set

 

NOS co-bound

353

Genes co-bound by Nanog, Oct4 and Sox2 in hESCs

 

Suz12 targets

1, 040

Genes bound by Suz12

Polycomb targets

Eed targets

1, 066

Genes bound by Eed

 

H3K27 bound

1, 121

Genes bound by H3K27

 

PRC2 targets

654

Overlap of three above sets

Myc targets

Myc targets1

230

E-box-containing genes regulated by c-Myc in cultured cell lines

 

Myc targets2

775

Genes commonly regulated by c-Myc and Max in a Burkitt's lymphoma cell line

P53 targets

 

35

Common gene lists regulated by p53 in mouse and human