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.

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

Lee et al. BMC Genomics 2007 8:441   doi:10.1186/1471-2164-8-441