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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.