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Table 3 ES – signature genes and coexpression with the neighboring genes. The genes in domains are arranged as they are on the chromosome from 5' to 3'.

From: Transcriptome coexpression map of human embryonic stem cells

Gene Chromosome Location Coexpression Index (ES) Coexpression Index (EB) Gene in Domain*** (20 Neighboring genes: 10 upstrea, 10 downstream)
FOXD3 1p32-p31 0.069 -0.083 INADL; FLJ10884; LOC163782; USP1; DOCK7; ANGPTL3; 400756; AUTL1; 199897; LOC199899; FOXD3; ALG6; ITGB3BP; PGM1; ROR1; 219612; MGC35130; KRTAP4–7; KIAA1573; KIAA1579; JAK1
TDGF1 3p21.31 -0.157 -0.016 401062; XCR1; CCR1; CCR3; CCR2; CCR5; CCRL2; LTF; TMEM7; LRRC2; TDGF1; FLJ36525; TMIE; TSP50; TESSP5; TESSP2; MYL3; PTHR1; MGC23918; HYPB; KIF9
SOX2 3q26.3–q27 0 0 GNB4; BAF53A; MRPL47; 133993; NDUFB5; USP13; PEX5R; TTC14; FXR1; LOC131118; SOX2; 401103; 402152; LOC142678; ATP11B; RP42; MCCC1; LAMP3; KIAA0861; B3GNT5; KLHL6
ABCG2 4q22 -0.039 -0.029 DHRS8; NUDT9; SPARCL1; DSPP; DMP1; LOC153218; IBSP; MEPE; SPP1; PKD2; ABCG2; DKFZp761G058; CEB1; MGC14156; DRLM; TIGD2; LOC285513; SNCA; MMRN; IRAK1BP1; TMSL3
LIFR 5p13-p12 0.187 -0.042 FLJ30596; FLJ25422; SLC1A3; IDN3; FLJ13231; NUP155; FLJ10233; GDNF; 147975; FLJ39155; LIFR; 253254; 401182; OSMR; MGC39830; FYB; C9; DAB2; PTGER4; OSRF; PRKAA1
IL6ST 5q11 0 0 GZMA; FLJ37927; 345643; UNG2; DHX29; KIAA0052; PPAP2A; FLJ90709; DDX4; CRL3; IL6ST; FLJ11795; 345645; MGC33648; FLJ35954; DKFZp761C169; 345651; SNK; FLJ33641; RAB3C; PDE4D
OCT3/4 6p21.31 0.102 0.23 IER3; DDR1; 389376; DPCR1; C6orf15; PSORS1C1; CDSN; PSORS1C2; C6orf18; TCF19; OCT3/4; LOC253018; HLA-C; HLA-B; MICA; HCP5; MICB; BAT1; ATP6V1G2; NFKBIL1; LTA
CER1 9p23-p22 -0.003 0.023 NIRF; GLDC; GASC1; PTPRD; TYRP1; 286343; MPDZ; 401492; NFIB; ZDHHC21; CER1; FLJ25461; C9orf52; SNAPC3; PSIP2; FLJ39267; C9orf39; SH3GL2; ADAMTSL1; FLJ35283; MGC35182
TLE1 9q21.32 0.084 0.285 PCSK5; FLJ11149; GCNT1; C9orf65; CHAC; GNA14; GNAQ; FLJ12643; PSAT1; TLE4; TLE1; FLJ43950; 389763; FLJ31614; MGC20553; UBQLN1; GKAP42; KIF27; C9orf64; HNRPK; C9orf76
NODAL 10q22.1 -0.001 -0.161 C10orf35; COL13A1; H2AFY2; AMID; MGC34695; SARA1; PP; OT7T022; FLJ10751; EIF4EBP2; NODAL; KIAA1274; PRF1; ADAMTS14; C10orf27; 338611; SGPL1; PCBD; UNC5B; SLC29A3; CDH23
UTF1 10q26 0.125 0.298 C10orf39; DPYSL4; PKE; LOC170394; LOC170393; INPP5A; NKX6-2; FLJ25954; GPR123; KIAA1768; UTF1; VENTX2; ADAM8; TUBGCP2; ZNF511; CALCYON; UPA; FLJ26016; ECHS1; PAOX; LOC92170
FGF4 11q13.3 -0.057 0 CPT1A; MRPL21; IGHMBP2; MRGD; MGC21621; TPCN2; MYEOV; CCND1; ORAOV1; FGF19; FGF4; FGF3; 399920; ORAOV2; FADD; PPFIA1; EMS1; SHANK2; 399921; LOC220070; DHCR7
NANOG 12p13.31 -0.06 0.007 RBP5; CLSTN3; PXR1; 341392; M160; CD163; APOBEC1; GDF3; DPPA3; CLECSF11; NANOG; SLC2A14; SLC2A3; FHX; C3AR1; DKFZP566B183; CLECSF6; FLJ10408; CLECSF8; CLECSF9; AICDA
STAT3 17q21 0.37 -0.171 201181; LGP2; GCN5L2; HspB9; RAB5C; KCNH4; HCRT; LGP1; STAT5B; STAT5A; STAT3; PTRF; ATP6V0A1; NAGLU; HSD17B1; DPCK; TCFL4; HUMGT198A; LOC162427; TUBG1; TUBG2
ERAS Xp11.23 -0.036 0.171 SLC38A5; FTSJ1; PPN; EBP; RBM3; WDR13; WAS; SUV39H1; GATA1; HDAC6; ERAS; PCSK1N; TIMM17B; PQBP1; SLC35A2; PIM2; DKFZp761A052; KCND1; TFE3; JM11; JM4
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