Table 2.
DEGseq analysis of marker genes as well as those highlighted in this study related to digit development
| Genes | Tag raw counts | Hand DII-V vs. Hand DI | Hand DII-V vs. Foot | Hand DI vs. Foot | |||||
|---|---|---|---|---|---|---|---|---|---|
| Hand DII-V | Hand DI | Foot | log2(Fold_change) normalized | p-value | log2(Fold_change) normalized | p-value | log2(Fold_change) normalized | p-value | |
| Marker genes | |||||||||
| Tbx5 | 175 | 134 | 6* | 0.326 | 0.048 | 5.6385 | 1.04E-57 | 5.3125 | 1.81E-45 |
| Pitx1 | 6 | 9 | 354* | -0.6441 | 0.3921 | -5.1104 | 4.08E-67 | -4.4663 | 3.04E-63 |
| Meis2 b | 73* | 12 | 18 | 2.5457 | 1.13E-11 | 2.7922 | 5.00E-17 | 0.2465 | 0.6365 |
| Hoxd10 b | 61* | 3 | 10 | 4.2866 | 1.09E-14 | 3.3811 | 5.17E-17 | -0.9056 | 0.289 |
| Krt17 ab | 68* | 267 | 455 | -2.3284 | 2.28E-40 | -1.9474 | 4.40E-38 | 0.381 | 0.0003 |
| Elongated digits | |||||||||
| Tbx3 b | 118* | 21 | 39 | 2.4312 | 4.16E-17 | 2.3695 | 2.10E-22 | -0.0617 | 0.8689 |
| Tbx15 b | 171* | 41 | 89 | 2.0011 | 2.79E-19 | 1.7144 | 2.10E-21 | -0.2868 | 0.2648 |
| Bmp3 b | 19* | 2 | 5 | 3.1888 | 1.04E-04 | 2.6983 | 2.64E-05 | -0.4905 | 0.6626 |
| Rgmb b | 727* | 133 | 289 | 2.3914 | 5.76E-95 | 2.1031 | 8.28E-112 | -0.2882 | 0.0435 |
| Smad1 | 264* | 122 | 250 | 1.0545 | 4.34E-12 | 0.8509 | 1.01E-11 | -0.2036 | 0.1782 |
| Smad4 | 412* | 244 | 351 | 0.6966 | 1.19E-09 | 1.0034 | 1.60E-22 | 0.3068 | 0.0086 |
| Nog a | 5** | 17 | 44 | -2.1207 | 1.53E-03 | -2.3427 | 6.61E-06 | -0.2219 | 0.5543 |
| Hoxd8 | 19* | 1 | 4 | 4.1888 | 1.81E-05 | 3.0202 | 8.64E-06 | -1.1686 | 0.4084 |
| Hoxd9 | 45* | 10 | 13 | 2.1108 | 1.88E-06 | 2.5637 | 3.17E-10 | 0.4529 | 0.4442 |
| Satb1 | 397* | 117 | 286 | 1.7035 | 1.48E-34 | 1.2454 | 3.85E-30 | -0.4581 | 0.0019 |
| Hoxa1 b | 61* | 14 | 12 | 2.0642 | 4.50E-08 | 3.118 | 5.91E-16 | 1.0538 | 0.0577 |
| Twist1 b | 2521* | 809 | 1767 | 1.5806 | 7.26E-189 | 1.285 | 4.31E-191 | -0.2957 | 3.08E-07 |
| Tmeff2 b | 95* | 22 | 50 | 2.0513 | 1.06E-11 | 1.6983 | 2.01E-12 | -0.353 | 0.3091 |
| Enpp2 b | 27* | 0 | 6 | 5.6957 | 8.71E-08 | 2.9422 | 1.64E-07 | -2.7535 | 0.0698 |
| Thumb &Foot | |||||||||
| Tbx4 ab | 20* | 102 | 390 | -2.7057 | 3.65E-19 | -3.4906 | 2.48E-60 | -0.7849 | 1.61E-08 |
| Pitx2 | 21* | 66 | 127 | -1.7112 | 3.08E-07 | -1.8241 | 6.16E-11 | -0.1129 | 0.589 |
| Acta1 ab | 412* | 1463 | 4918 | -2.1834 | 1.81E-197 | -2.7825 | 0 | -0.5991 | 9.29E-57 |
| Tnnc2 b | 115* | 534 | 1544 | -2.2744 | 5.62E-69 | -2.9747 | 6.36E-204 | -0.7003 | 4.41E-26 |
| Atp2a1 | 17* | 103 | 223 | -2.6582 | 3.49E-17 | -2.9412 | 1.12E-30 | -0.283 | 0.0813 |
| Hrc | 9* | 40 | 67 | -2.2112 | 2.34E-06 | -2.1239 | 1.52E-07 | 0.0873 | 0.7535 |
| Myoz1 | 8* | 34 | 58 | -2.1466 | 1.93E-05 | -2.0857 | 1.37E-06 | 0.0609 | 0.8391 |
a, homologs of mouse genes, all others are the homologs of human genes; b, genes expression patterns validated by RT-qPCR; * indicates gene expression in the library is significantly higher or lower than in other two libraries (*, p < 0.001; **, p < 0.01).