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Table 5 Overlaps between the 24 hESC-associated gene sets and the 72 differentially expressed gene sets

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

Gene sets

#Genes with 10 or more overlapsb

Top 10 overlapping genes

hESC exp1

308 (81%)

MTHFD2, MCM4, MCM6, LGALS8, PPP2R1B, RFC4, GART, BUB1, LCK, PTPN2

hESC exp2

26 (65%)

MYBL2, EPHA1, ORC2, DTYMK, PRKD3, NCAPH, ETV4, DSCC1, CDC25A, PWP2

hESC exp3

38 (79%)

BUB1, DLGAP5, SLC16A1, USP9X, HSPA4, TERF1, PSIP1, PLA2G16, UGP2, BMPR1A

hESC exp4

29 (97%)

SPARC, COL1A2, COL3A1, COL1A1, CD47, COL5A2, KRT18, KRT8, LUM, COL6A3

hESC exp5

135 (71%)

TCF4, STAT1, GATA3, MAF, MYC, MYBL2, ILF3, SMAD4, FUBP1, GATA2

hESC exp6

28 (64%)

CD9, IL6ST, PTEN, EDNRB, KIT, NR5A2, IFITM2, CRABP2, NFYC, PODXL

hESC exp7

863 (87%)

GNAS, FN1, SPARC, MCM6, MCM4, TOP2A, COL1A2, COL3A1, RFC4, RAB31

hESC exp8

11 (50%)

FAS, CKS1B, GJA1, NPM1, TGIF1, HMGA1, DNMT3A, ERH, SOX2, DNMT3B

hESC exp9

21 (78%)

PCNA, CKS1B, FAS, TERF1, GJA1, CCNB1, NPM1, FZD7, SFRP1, HMGA1

hESC exp10

30 (97%)

PGK1, BAK1, HNRNPA1, EEF1A1, PPIA, GAPDH, GJA1, TMED2, EEF1B2, NPM1

hESC exp11

749 (75%)

PDE4DIP, FGFR2, CKS2, MTHFD2, SOX4, SLC2A3, STAT1, MAPK1, PSMB2, MCM4

Nanog targets

711 (72%)

CALD1, FGFR2, CKS2, TNPO1, KIAA0101, SPARC, TOP2A, ARHGAP1, B2M, VCAN

Oct4 targets

211 (73%)

FGFR2, TCF4, KIAA0101, TOP2A, PPP2R1B, TCF12, UBE2D3, RAB5A, HMGB2, PTPN2

Sox2 targets

542 (74%)

FGFR2, TOP2A, ARHGAP1, VCAN, PPP2R1B, UBE2D3, CBX3, RAB5A, PIK3R3, H2AFX

NOS targets

132 (74%)

FGFR2, TOP2A, PPP2R1B, UBE2D3, RAB5A, PTPN2, SET, FGFR1, BUB3, ADD3

NOS TFs

28 (76%)

STAT3, MYST3, IFI16, MLLT10, FOXO1, PHF17, ZFP36L1, TAF12, HHEX, ZEB2

NOS co-bound

199 (56%)

FGFR2, TOP2A, PPP2R1B, UBE2D3, RAB5A, PTPN2, SET, FGFR1, BUB3, BMI1

Suz12 targets

512 (49%)

PDE4DIP, BCL2, GNAS, PTGER3, CD44, RAB31, CYP1B1, EPHB1, GATA3, HLF

Eed targets

510 (48%)

PDE4DIP, BCL2, PTGER3, PRKCB, CD44, INPP4A, CYP1B1, EPHB1, GATA3, HLF

H3K27 bound

557 (50%)

PDE4DIP, BCL2, PTGER3, PRKCB, EPHB1, GATA3, NTRK2, CD47, GPD1L, NCAM1

PRC2 targets

397 (61%)

PDE4DIP, BCL2, PTGER3, EPHB1, GATA3, NTRK2, NCAM1, CACNA1D, GATA2, GPM6B

Myc targets1

204 (89%)

BCL2, MCM4, TGFB3, CCND2, APC, MUC1, TCF12, ENO1, APP, CSTB

Myc targets2

645 (83%)

CKS2, PPP2R1B, TCF12, UBE2D3, CDC25B, H2AFX, HLA-A, PDK3, PRKDC, TMF1

P53 targets

27 (77%)

GATM, MYH11, TP53, BTG2, INPP5D, MDM2, MYB, SPARCL1, PLK4, FMO5

  1. b The percentage of the overlapping gene number relative to the total gene number for each of the 24 hESC-associated gene sets is given in parenthesis.