| Positive correlation | Negative correlation | ||
| Gene | r | Gene | r |
| fezf2 | 0.312 | meis1b | -0.122 |
| dmrta2 | 0.223 | hoxb3a | -0.112 |
| nkx2.4b | 0.215 | hoxb9a | -0.098 |
| wnt8b | 0.212 | hoxc3a | -0.096 |
| pitx3 | 0.187 | si:ch73-265d7.2 | -0.089 |
| ccl44 | 0.159 | hoxb8a | -0.087 |
| foxg1a | 0.150 | vim | -0.084 |
| barhl1a | 0.150 | hoxb1b | -0.080 |
| pitx2 | 0.142 | hoxd3a | -0.078 |
| lhx2b | 0.141 | hoxc9a | -0.075 |
| nkx2.4a | 0.140 | hoxa3a | -0.075 |
| slc1a3b | 0.138 | hoxb7a | -0.074 |
| zgc:165461 | 0.136 | hoxd9a | -0.072 |
| emx3 | 0.136 | hoxa9a | -0.072 |
| barhl1b | 0.131 | hoxc8a | -0.071 |
| ptprn2 | 0.130 | hoxa9b | -0.066 |
| shha | 0.129 | meis1a | -0.066 |
| nell2a | 0.128 | hoxb10a | -0.066 |
| otx2a | 0.125 | hoxa10b | -0.066 |
| tnfrsf19 | 0.120 | pax3a | -0.065 |
| otx1 | 0.118 | hoxc1a | -0.064 |
| nr2e1 | 0.114 | elavl3 | -0.063 |
| grm2b | 0.111 | hoxc6b | -0.062 |
| nkx2.1 | 0.111 | znf503 | -0.061 |
| wls | 0.109 | cdkn1ca | -0.058 |
| marcksl1a | 0.105 | calm2a | -0.058 |
| CR751602.2 | 0.104 | serinc5 | -0.056 |
| wnt7bb | 0.101 | meis2b | -0.056 |
| CU467822.1 | 0.098 | raraa | -0.056 |
| BX322555.3 | 0.097 | slc1a3a | -0.056 |
| wnt7ba | 0.096 | marcksl1b | -0.055 |
| ntrk2a | 0.096 | col11a1a | -0.055 |
| LOC103909284 | 0.095 | cadm4 | -0.055 |
| si:dkey-274m17.3 | 0.094 | tmeff1b | -0.055 |
| id3 | 0.094 | hoxd10a | -0.055 |