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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.

From: TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements

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