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Table 3 Top twenty TF-encoding genes associated with the highest number and total length 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.

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

Gene ID Gene name Description Number of CNEs Length of CNEs (kb)
ENSG00000134138 MEIS2 Homeobox protein Meis2 79 11.98
ENSG00000177508 IRX3 Iroquois-class homeodomain protein IRX-3 68 10.87
ENSG00000169554 ZFHX1B Zinc finger homeobox protein 1b 76 10.25
ENSG00000143032 BARHL2 BarH-like 2 homeobox protein. 56 10.09
ENSG00000169946 ZFPM2 Zinc finger protein ZFPM2 49 9.90
ENSG00000167081 PBX3 Pre-B-cell leukemia transcription factor 3 57 9.10
ENSG00000091656 ZFHX4 zinc finger homeodomain 4 77 9.05
ENSG00000151514 SALL3 Sal-like protein 3 59 8.94
ENSG00000170549 IRX1 Iroquois-class homeodomain protein IRX-1 48 8.67
ENSG00000128573 FOXP2 Forkhead box protein P2 57 8.41
ENSG00000121297 ZNF537 Teashirt homolog 3 59 7.38
ENSG00000143995 MEIS1 Homeobox protein Meis1. 63 7.00
ENSG00000148737 TCF7L2 Transcription factor 7-like 2 42 6.91
ENSG00000153234 NR4A2 Orphan nuclear receptor NR4A2 38 6.73
ENSG00000159387 IRX6 Iroquois-class homeodomain protein IRX-6 40.5 6.54
ENSG00000176842 IRX5 Iroquois-class homeodomain protein IRX-5 40.5 6.54
ENSG00000110693 SOX6 Transcription factor SOX-6. 47 6.41
ENSG00000143013 LMO4 LIM domain transcription factor LMO4 32 5.92
ENSG00000164853 XP_496843.1 PREDICTED: similar to Uncx4.1 31 5.74
ENSG00000075891 PAX2 Paired box protein Pax-2. 37 5.68