Table 1

Identified genes with altered methylation in zebrafish HCC.

Gene name

Gene ID

Chr. no

CGI region


A. Hypomethylated Genes

Proliferation

Kruppel-like factor 12b

ENSDARG00000032197

9

31117162 - 31117483

Insulin-like growth factor binding protein 5a

ENSDARG00000025348

9

49194032 - 49194791

Insulin-like growth factor binding protein 2a

ENSDARG00000031422

9

49290381 - 49290816

Insulin-like growth factor binding protein 1b

ENSDARG00000038666

2

178184 - 178306

Insulin-like growth factor-binding protein 2A precursor

ENSDARG00000052470

6

22745784 - 22746301

Estrogen related receptor delta fragment

ENSDARG00000015064

18

48225445 - 48225631

Hypothetical protein LOC550398

ENSDARG00000043587

1

51038733 - 51038845

Stress

Similar to SH2 domain containing 3C

ENSDARG00000028099

10

14303115 - 14303263

PI-kinase-related SMG-1

ENSDARG00000054570

3

28544220 - 28544532

Glycolysis

Enolase 2

ENSDARG00000014287

19

4698036 - 4698168

Hexokinase 1

ENSDARG00000039452

13

23684991 - 23685203

Cell cycle, metastasis, adhesion, cell growth, stress

c-Jun protein

ENSDARG00000043531

20

14274343 - 14274635

BCL2-associated athanogene 5

ENSDARG00000017316

13

17324708 - 17324877

Angiopoietin-like 3

ENSDARG00000044365

6

34165085 - 34165237

Angiopoietin-1 receptor precursor

ENSDARG00000028663

5

625275 - 625436

Ras homolog gene family, member Ua

ENSDARG00000019709

13

25136705 - 25136882

Menage a trois homolog 1

ENSDARG00000002077

13

31141636 - 31142019

Serine/threonine and tyrosine protein kinase

ENSDARG00000000853

22

461194 - 461772

DNA binding and regulation of transcription

DNA (cytosine-5-)-methyltransferase 6

ENSDARG00000015566

17

34759411 - 34759539

Leucine zipper protein 2 precursor

ENSDARG00000068247

18

35625841 - 35625986

Histone H2A

ENSDARG00000001915

1

724191 - 724473

Histone deacetylase 4

ENSDARG00000041204

9

46375505 - 46375895

Homeobox protein Hox-B5a

ENSDARG00000013057

3

20707021 - 20707754

Pancreas transcription factor 1 subunit alpha

ENSDARG00000014479

2

27672474 - 27672641

Hypothetical protein LOC692291

ENSDARG00000012833

17

12689887 - 12690054

Metastasis associated 1 family, member 2

ENSDARG00000013031

7

17243535 - 17244290

Homeobox protein Hox-B4a

ENSDARG00000013533

3

20721064 - 20721722

Lysine-specific demethylase 4A

ENSDARG00000018782

6

4575451 - 4575994

RAB11 family interacting protein 4 (class II) a

ENSDARG00000053855

25

13380260 - 13380369

B. Hypermethylated Genes

Anti-angiogenesis

Hematopoietically-expressed homeobox protein hhex

ENSDARG00000074250

12

43558447 - 43558684

Cell-cell adhesion

Hypothetical protein LOC678612

ENSDARG00000069505

21

27963202 - 27963305

Novel protocadherin protein fragment

ENSDARG00000053462

1

55112983 - 55113251

Transporter

ATP-binding cassette, sub-family A, member 5

ENSDARG00000074041

12

38940033 - 38940251

immune system

Novel protein similar to nuclear factor, interleukin 3 regulated

ENSDARG00000071398

22

21400978 - 21401243

Novel protein fragment

ENSDARG00000053462

1

55112983 - 55113251

C5a anaphylatoxin chemotactic receptor

ENSDARG00000040319

18

45692130 - 45692420

Angiogenesis and oxidative stress protection

Vascular endothelial zinc finger 1

ENSDARG00000008247

10

35492470 - 35493037

Membrane

Coronin, actin binding protein 2ba

ENSDARG00000079440

7

33649014 - 33649398


A. Genes identified as hypomethylated in HCC as measured by CGI-tiling array (1.5-fold less methylation in tumor samples than controls, P-value < 0.05). B. Genes identified as hypermethylated in HCC as measured by CGI-tiling array (1.5-fold more methylation in tumor samples than controls, P-value < 0.05). Full data is shown in Additional file 6, Tables S2 and S3.

Mirbahai et al. BMC Genomics 2011 12:3   doi:10.1186/1471-2164-12-3

Open Data