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

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