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


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

Open Data