| Positive correlation | Negative correlation | ||
| Gene | r | Gene | r |
| pitx3 | 0.418 | meis1b | -0.120 |
| shha | 0.303 | hoxb3a | -0.114 |
| lmx1ba | 0.236 | hoxb9a | -0.105 |
| foxa2 | 0.234 | hoxc3a | -0.102 |
| foxa1 | 0.224 | vim | -0.093 |
| emx2 | 0.223 | hoxb8a | -0.090 |
| tmem88b | 0.210 | hoxd3a | -0.087 |
| otx2a | 0.186 | hoxb1b | -0.085 |
| barhl1a | 0.183 | si:ch73-265d7.2 | -0.082 |
| barhl1b | 0.178 | hoxc9a | -0.081 |
| lmx1bb | 0.164 | hoxa3a | -0.080 |
| arxa | 0.162 | hoxb7a | -0.077 |
| pitx2 | 0.159 | calm2a | -0.075 |
| si:dkey-208c12.2 | 0.142 | hoxc8a | -0.075 |
| foxa | 0.140 | hoxd9a | -0.074 |
| otx1 | 0.139 | hoxa9a | -0.074 |
| epha7 | 0.138 | znf503 | -0.072 |
| sema3bl | 0.135 | hoxa9b | -0.070 |
| CR751602.2 | 0.132 | pax3a | -0.070 |
| ntn1b | 0.130 | gng3 | -0.070 |
| irx1a | 0.127 | hoxa10b | -0.069 |
| pcbd1 | 0.127 | hoxb10a | -0.068 |
| sox11a | 0.126 | ptmaa | -0.068 |
| si:ch211-212k18.5 | 0.126 | elavl4 | -0.068 |
| foxg1a | 0.122 | meis1a | -0.067 |
| fgfr3 | 0.121 | hoxc1a | -0.067 |
| LOC103911485 | 0.120 | hoxc6b | -0.066 |
| lrrn1 | 0.117 | stx1b | -0.066 |
| ntn1a | 0.115 | stxbp1a | -0.065 |
| vasna | 0.114 | snap25a | -0.064 |
| cldn5a | 0.114 | sncb | -0.064 |
| her2 | 0.113 | gpm6ab | -0.064 |
| podxl | 0.111 | atp6v0cb | -0.064 |
| emx3 | 0.111 | meis2a | -0.063 |
| wls | 0.110 | nsg2 | -0.062 |