Table 1.
Differentially expressed TFs
| HECs versus ECs | HSCs versus HECs | HSCs versus ECs | ||||||
| Gene | logFC | FDR | Gene | logFC | FDR | Gene | logFC | FDR |
| (A) Top 25 up-regulated genes | ||||||||
| Elk3 | 2.42 | 1.1E-02 | Myb | 4.23 | 1.7E-06 | Myb | 4.55 | 7.1E-08 |
| Mecom | 3.21 | 1.4E-02 | Gfi1b | 5.48 | 7.7E-05 | Ikzf2 | 3.13 | 2.5E-04 |
| Notch4 | 5.41 | 2.9E-02 | Hlf | 7.03 | 8.9E-05 | Hlf | 5.99 | 6.7E-04 |
| Notch1 | 2.16 | 4.2E-02 | Meis1 | 2.20 | 8.1E-04 | Runx1 | 2.68 | 1.8E-03 |
| Rab11a | 2.03 | 5.2E-02 | Zfp106 | 2.43 | 3.5E-03 | Myc | 2.27 | 9.5E-03 |
| Gfi1 | 7.69 | 6.8E-02 | Ncoa4 | 2.05 | 8.8E-03 | Dnmt3a | 1.73 | 2.2E-02 |
| Wwtr1 | 3.20 | 6.8E-02 | Nop2 | 2.35 | 1.9E-02 | Chd4 | 1.62 | 2.9E-02 |
| Junb | 4.90 | 6.8E-02 | Elf1 | 2.51 | 2.0E-02 | Dnmt1 | 1.58 | 3.2E-02 |
| Ets2 | 2.50 | 6.9E-02 | Zfp445 | 2.05 | 2.3E-02 | Gfi1 | 8.33 | 3.3E-02 |
| Mapk3 | 1.62 | 7.3E-02 | Nfe2 | 5.05 | 4.1E-02 | Zfp445 | 1.91 | 4.6E-02 |
| Nkx2-3 | 5.95 | 7.4E-02 | Zfp763 | 4.29 | 4.2E-02 | Setbp1 | 2.78 | 5.9E-02 |
| Ldb2 | 2.30 | 7.5E-02 | Ikzf2 | 1.94 | 5.2E-02 | Ikzf1 | 2.60 | 6.8E-02 |
| Hdac7 | 2.20 | 7.6E-02 | Huwe1 | 1.55 | 5.7E-02 | Bcor | 2.21 | 8.4E-02 |
| Sox17 | 5.14 | 8.4E-02 | Orc2 | 2.22 | 6.5E-02 | Trp53bp1 | 1.51 | 8.5E-02 |
| Ctnnb1 | 1.28 | 9.5E-02 | Mpl | 2.84 | 6.6E-02 | Mycn | 2.57 | 9.9E-02 |
| Hey1 | 4.24 | 1.1E-01 | Etv6 | 1.99 | 6.9E-02 | Zfp106 | 1.67 | 1.0E-01 |
| Epas1 | 3.10 | 1.2E-01 | Lmo1 | 8.87 | 7.5E-02 | Suz12 | 1.57 | 1.1E-01 |
| Hey2 | 4.35 | 1.2E-01 | Paxip1 | 1.93 | 7.6E-02 | Cbfa2t3 | 2.63 | 1.2E-01 |
| Sox7 | 4.27 | 1.5E-01 | Cpsf6 | 1.28 | 8.1E-02 | Paxip1 | 1.83 | 1.4E-01 |
| Sox18 | 4.05 | 1.5E-01 | Zfp748 | 2.68 | 8.3E-02 | Notch1 | 1.72 | 1.4E-01 |
| Tsc22d1 | 1.46 | 1.6E-01 | Polr1a | 2.41 | 8.3E-02 | Etv6 | 1.82 | 1.5E-01 |
| Nrarp | 3.76 | 1.7E-01 | Trp53bp1 | 1.42 | 8.9E-02 | Kdm5a | 1.38 | 1.5E-01 |
| Nfic | 2.07 | 1.8E-01 | Dnmt1 | 1.29 | 9.4E-02 | Meis1 | 1.22 | 1.8E-01 |
| Pdlim1 | 1.96 | 2.1E-01 | Med23 | 1.84 | 9.8E-02 | Rreb1 | 1.49 | 1.8E-01 |
| Hmg20b | 2.46 | 2.1E-01 | Krr1 | 1.45 | 1.0E-01 | Bptf | 1.17 | 1.8E-01 |
| (B) Top 25 down-regulated genes | ||||||||
| Pou5f1 | −7.70 | 2.6E-04 | Snai2 | −7.39 | 7.7E-05 | Snai2 | −8.64 | 3.0E-06 |
| Utf1 | −8.22 | 1.0E-02 | Id3 | −3.87 | 5.6E-04 | Rhox6 | −10.09 | 2.9E-05 |
| Gfi1b | −3.77 | 1.3E-02 | Hey2 | −7.55 | 2.3E-03 | Rhox9 | −10.23 | 4.6E-05 |
| Foxd1 | −10.54 | 6.6E-02 | Rhox6 | −6.49 | 6.8E-03 | Tgfb1i1 | −5.76 | 4.6E-05 |
| Lmo1 | −10.20 | 6.7E-02 | Msx2 | −8.54 | 7.4E-03 | Pou5f1 | −7.16 | 2.2E-04 |
| Hand1 | −6.55 | 7.4E-02 | Rhox9 | −6.56 | 9.0E-03 | Etv5 | −3.26 | 6.0E-04 |
| Zfp612 | −7.77 | 1.0E-01 | Etv5 | −2.60 | 1.1E-02 | Utf1 | −8.47 | 3.6E-03 |
| Prrx2 | −7.19 | 1.0E-01 | Isl1 | −4.08 | 3.6E-02 | Msx2 | −8.98 | 5.1E-03 |
| Asb12 | −9.04 | 1.1E-01 | Ebf2 | −7.43 | 4.0E-02 | Id3 | −3.21 | 5.8E-03 |
| Cdc6 | −1.75 | 1.3E-01 | Ebf1 | −5.39 | 4.3E-02 | Prrx2 | −10.99 | 6.9E-03 |
| Ncoa4 | −1.48 | 1.4E-01 | Hey1 | −4.69 | 4.4E-02 | Prss35 | −5.99 | 1.8E-02 |
| Krr1 | −1.47 | 1.4E-01 | Epas1 | −3.42 | 4.6E-02 | Grhl3 | −6.02 | 2.6E-02 |
| Alx4 | −5.93 | 1.5E-01 | Rarb | −3.81 | 5.2E-02 | Foxd1 | −10.54 | 2.8E-02 |
| Wt1 | −4.76 | 2.0E-01 | Hoxd9 | −7.63 | 5.5E-02 | Ripk4 | −9.34 | 3.0E-02 |
| Rhox2e | −3.29 | 2.0E-01 | Sox17 | −5.00 | 5.7E-02 | Ebf2 | −8.08 | 3.0E-02 |
| Pax8 | −8.85 | 2.1E-01 | Creb3l1 | −4.59 | 5.8E-02 | Foxp2 | −3.93 | 3.4E-02 |
| Rhox6 | −3.59 | 2.2E-01 | Ugp2 | −1.79 | 6.5E-02 | Zim1 | −7.30 | 3.4E-02 |
| Neurod6 | −6.02 | 2.2E-01 | Nr3c1 | −2.93 | 6.9E-02 | Creb3l1 | −5.25 | 3.5E-02 |
| Hoxc4 | −8.73 | 2.3E-01 | Notch4 | −4.21 | 7.1E-02 | Hoxd9 | −8.66 | 3.6E-02 |
| Rhox9 | −3.68 | 2.3E-01 | Myt1 | −6.02 | 7.6E-02 | Sall4 | −2.66 | 3.8E-02 |
| Six1 | −7.30 | 2.3E-01 | Elf3 | −6.86 | 7.6E-02 | Id2 | −2.69 | 3.9E-02 |
| Tcf21 | −5.63 | 2.3E-01 | Ankrd1 | −4.84 | 7.7E-02 | Hoxc10 | −5.83 | 5.0E-02 |
| Runx1t1 | −1.79 | 2.4E-01 | Onecut3 | −8.32 | 8.3E-02 | Myt1 | −6.64 | 6.7E-02 |
| Klf1 | −6.56 | 2.6E-01 | Hivep3 | −5.19 | 8.4E-02 | Elf3 | −7.56 | 6.9E-02 |
| Aff3 | −3.18 | 3.1E-01 | Zfp36l1 | −1.90 | 8.6E-02 | Isl1 | −3.79 | 7.0E-02 |
(A and B) Top 25 up-regulated TFs (A) and top 25 down-regulated TFs (B) in HEC versus EC, HSC versus HEC, and HSC versus EC comparisons. FDR, FDR corrected p-value; logFC, log fold change. All genes with FDR < 0.05 except genes with underlining.