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Table 2 Major functional categories of the four subclusters from the hierarchical clustering (Figure 2b) and the respective genes

From: Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis

Subcluster Genes Function
1a Lefty1, Lefty2, Nr0b1, Mcf2, Notch4, Metabolism
  Foxh1, Ubtf, Gtf2i, Tdh, Upp1, Fkbp9, Development: embryonic, tube
  Enpp3, Socs2, Cacna1a, Pycard, Enah, Morphogenesis
  Lef1, Esrrb, Rnf125, Ddc, Bcat1, Dpp4, Pattern specification
  Ptpmt1, Ctbp2, Pml, Ptbp2, Hnrpa2b1 Cell differentiation
   Growth
1b Nanog, Tbx3, Sall1, Gdf3, Klf3, Klf4, Metabolism
  Zic3, Zic5, FoxD3, Gli2, Gja1, Otx2, Transcription
  Zbtb7a, Nsd1, Arid1a, NFIb, Pitx2, Rarg, Suv39H1, Cul1, Ppap2b, Pdgfc, Tns3, Development: embryonic, organ, tube
  Inhbb, Fn1, Tcfap4, Nr5a2, MllT6, Irf2bp2, Pcaf, Zfp42, Zmynd11, Ncor1, Morphogenesis: embryonic, organ, tube
  MllT10, Tgif, Trps1, Emp1, Pkd2, Spry2, Cell proliferation
  Gjb3, Fgf4, Vegfc, Hsd17B11, Cbr3, Growth
  Fbxo15, Dusp27, Frrs1, Cdk6, Epb4.9, Irak3, Spry4, Manba, Folr1  
2a Sema4f, Mbp, Cnp, Stxbp1, Hoxa1, Fos, Farp2, Sept4, Krt1-18, H1f0, Tubb2a, Cell organization and biogenesis
  Dnajc12, Cenpj, Spire1, Pappa2, Sh2b2, Tax1bp3, Rnd1, Arhgap29, Edg3, Mknk2, Errf1, Rap40b, Pdgfrb System development: nervous system development; neurogenesis; cell development
   Intracellular signaling
2b Id2, Id4, Wif1, Hoxb13, Prkar1b, Prkar2b, Metabolism
  Zfp36, Cd74, Thy1, Serpine1, Dhcr7, Pdlim7, Ctgf, Mlf1, Lgals1, Kif3a, Irf8, Hsdl2, H1h2bf, H1h2bp, H1h2bc, H2h3c1, Junb, Cbx4, Hspa1a, Hspa1b, Hspa2, Acaa1b, H1fx, Psmb9, H2-T3, H2-K1, Hist1h2bn Development: organ development/morphogenesis; vasculature development; angiogenesis; hemopoiesis/blood vessel development
   Cell differentiation
   Chromosome organization
   Immune response