Table 2.
Top twenty TF-encoding genes associated with the highest density of human-fugu CNEs. For genes that are part of conserved clusters, we averaged out the number or length of CNEs present in the whole cluster over the number of genes in that cluster. CNE density is defined here as the number of bases located in CNEs per kilobase of non-repetitive noncoding sequence in a gene locus.
| Gene ID | Gene name | Description | CNE bases per kb of human sequence |
| ENSG00000164853 | XP_496843.1 | PREDICTED: similar to Uncx4.1 | 37.61 |
| ENSG00000188620 | XP_291716.5 | PREDICTED: similar to homeodomain protein | 31.82 |
| ENSG00000188816 | NP_005510.1 | Homeobox (H6 family) 2 | 31.82 |
| ENSG00000166407 | LMO1 | Rhombotin-1 | 29.17 |
| ENSG00000167081 | PBX3 | Pre-B-cell leukemia transcription factor 3 | 29.16 |
| ENSG00000130940 | CASZ1 | Probable transcription factor CST | 26.43 |
| ENSG00000139800 | ZIC5 | Zinc finger protein ZIC 5 | 25.94 |
| ENSG00000109132 | PHOX2B | Paired mesoderm homeobox protein 2B | 24.93 |
| ENSG00000075891 | PAX2 | Paired box protein Pax-2. | 24.27 |
| ENSG00000177508 | IRX3 | Iroquois-class homeodomain protein IRX-3 | 24.04 |
| ENSG00000165655 | ZNF503 | zinc finger protein 503 | 21.39 |
| ENSG00000143032 | BARHL2 | BarH-like 2 homeobox protein. | 21.28 |
| ENSG00000171540 | OTP | orthopedia | 21.25 |
| ENSG00000125285 | SOX21 | Transcription factor SOX-21 | 19.99 |
| ENSG00000159387 | IRX6 | Iroquois-class homeodomain protein IRX-6 | 19.51 |
| ENSG00000176842 | IRX5 | Iroquois-class homeodomain protein IRX-5 | 19.51 |
| ENSG00000134138 | MEIS2 | Homeobox protein Meis2 | 18.05 |
| ENSG00000128652 | HOXD3 | Homeobox protein Hox-D3 | 17.34 |
| ENSG00000128709 | HOXD9 | Homeobox protein Hox-D9 | 17.34 |
| ENSG00000128710 | HOXD10 | Homeobox protein Hox-D10 | 17.34 |