Table 1 Methylated target genes identified by methylated-CpG island recovery assay-assisted microarray analysis
From: Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer
Target number | Gene | Description | Gene location | Strand | Position relative to genea | Average ratiob | Count |
|---|---|---|---|---|---|---|---|
1* | FOXE1 | Forkhead box E1 | Chr9: 99655357 to 99658818 | + | Downstream | 13.76 | 4 |
2 | SEMA6C | Semaphorin 6C | Chr1: 149370786 to 149385728 | - | Downstream | 6.40 | 4 |
3* | HNF1B c | Hnf1 homeobox B | Chr17: 33120546 to 33179209 | - | Upstream | 6.06 | 4 |
4 | OTX1 | Orthodenticle homeobox 1 | Chr2: 63131468 to 63137816 | + | Intragenic | 4.83 | 4 |
5* | TLX1 | T-cell leukemia homeobox 1 | Chr10: 102881050 to 102887535 | + | Intragenic | 4.50 | 4 |
6 | ESAM | Endothelial cell adhesion molecule | Chr11: 124128228 to 124137433 | - | Intragenic | 4.16 | 4 |
7* | CNTNAP1 | Contactin associated protein 1 | Chr17: 38088158 to 38105358 | + | Intragenic | 3.94 | 4 |
8* | GFI1 | Growth factor independent 1 transcription repressor | Chr1: 92712905 to 92725021 | - | Intragenic | 3.64 | 4 |
9* | RASL10A | Ras-like, family 10, member A | Chr22: 28038921 to 28041748 | - | Intragenic | 3.42 | 4 |
10* | IFNA8 | Interferon, alpha 8 | Chr9: 21399146 to 21400184 | + | Upstream | 3.41 | 4 |
11 | ERGIC2 | Ergic and golgi 2 | Chr12: 29384845 to 29425410 | - | Upstream | 3.39 | 4 |
12 | PCDH7 | Protocadherin 7 | Chr4: 30331134 to 30757519 | + | Intragenic | 3.16 | 4 |
13 | RASGRP2 | Ras guanyl releasing protein 2 | Chr11: 64250958 to 64269504 | - | Intragenic | 3.01 | 4 |
14 | NFATC1 | Nuclear factor of activated T-cells 1 | Chr18: 75256759 to 75390311 | + | Intragenic | 2.93 | 4 |
15 | RLTPR | Rgd motif, leucine-rich repeats, tropomodulin domain and proline-rich containing gene | Chr16: 66236530 to 66248973 | + | Intragenic | 2.75 | 4 |
16 | AK123344 | Hypothetical gene | Chr10: 102979341 to 102985256 | + | Downstream | 16.49 | 3 |
17 | C1orf114 | Chromosome 1 open reading frame 114 | Chr1: 167630737 to 167663294 | - | Upstream | 11.13 | 3 |
18 | TRPS1 | Trichorhinophalangeal syndrome I | Chr8: 116489899 to 116750402 | - | Intragenic | 11.07 | 3 |
19 | PCDHGA12 | Protocadherin gamma subfamily A, 12 | Chr5: 140790341 to 140872730 | + | Upstream | 11.02 | 3 |
20 | C14orf25 | Chromosome 14 open reading frame 25 | Chr14: 37150207 to 37580397 | + | Upstream | 10.34 | 3 |
21 | CDKN2A | Cyclin-dependent kinase inhibitor 2A (P16) | Chr9: 21957750 to 21984490 | - | Downstream | 9.86 | 3 |
22 | SCRT2 | Scratch homolog 2, zinc finger protein | Chr20: 590240 to 604823 | - | Downstream | 9.47 | 3 |
23 | BCOR | Bcl6 co-repressor | Chrx: 39795443 to 39921526 | - | Upstream | 9.43 | 3 |
24 | KHDC1 | Kh homology domain containing 1 | Chr6: 74007759 to 74076659 | - | Upstream | 9.00 | 3 |
25* | NXPH1 | Neurexophilin 1 | Chr7: 8440109 to 8759118 | + | Intragenic | 8.83 | 3 |
26 | CNR1 | Cannabinoid receptor 1 (brain) | Chr6: 88910156 to 88932281 | - | Upstream | 8.78 | 3 |
27 | BC039088 | Hypothetical gene | Chr5: 43050280 to 43054670 | - | Upstream | 8.61 | 3 |
28 | EVX2 | Even-skipped homeobox 2 | Chr2: 176653080 to 176656936 | - | Downstream | 8.43 | 3 |
29* | MT1E | Metallothionein 1E | Chr16: 55217085 to 55218525 | + | Upstream | 8.36 | 3 |
30* | NR2F2 | Nuclear receptor subfamily 2, group F, member 2 | Chr15: 94674950 to 94683047 | + | Downstream | 8.24 | 3 |
31 | HOXC13 | Homeobox C13 | Chr12: 52618843 to 52626595 | + | Upstream | 8.08 | 3 |
32 | HOXD8 | Homeobox D8 | Chr2: 176702722 to 176704974 | + | Upstream | 7.97 | 3 |
33 | SYCP2L | Synaptonemal complex protein 2-like | Chr6: 10995049 to 11082527 | + | Upstream | 7.58 | 3 |
34 | PCDHGB6 | Protocadherin gamma subfamily B, 6 | Chr5: 140767953 to 140872730 | + | Intragenic | 7.37 | 3 |
35 | ACTA1 | Actin, alpha 1, skeletal muscle | Chr1: 227633615 to 227636466 | - | Upstream | 7.36 | 3 |
36* | PRDM14 | Pr domain containing 14 | Chr8: 71126576 to 71146116 | - | Intragenic | 7.27 | 3 |
37* | HOXB13 | Homeobox B13 | Chr17: 44157124 to 44161110 | - | Intragenic | 6.91 | 3 |
38 | OTX2 | Orthodenticle homeobox 2 | Chr14: 56337177 to 56346937 | - | Upstream | 6.70 | 3 |
39 | ZNF711 | Zinc finger protein 711 | Chrx: 84385652 to 84415025 | + | Upstream | 6.63 | 3 |
40* | NR2E1 | Nuclear receptor subfamily 2, group E, member 1 | Chr6: 108593954 to 108616706 | + | Intragenic | 6.44 | 3 |
41* | TAC1 | Tachykinin, precursor 1 | Chr7: 97199206 to 97207720 | + | Upstream | 6.37 | 3 |
42* | CPEB1 | Cytoplasmic polyadenylation element binding protein 1 | Chr15: 81009005 to 81113783 | - | Upstream | 5.99 | 3 |
43 | NKAPL | Nfkb activating protein-like | Chr6: 28335076 to 28336715 | + | Upstream | 5.86 | 3 |
44 | NKX6-2 | Nk6 homeobox 2 | Chr10: 134448309 to 134449527 | - | Downstream | 5.72 | 3 |
45* | TGIF2 | Tgfb-induced factor homeobox 2 | Chr20: 34635423 to 34655766 | + | Upstream | 5.60 | 3 |
46 | CR596471 | Hypothetical gene | Chrx: 133511720 to 133522094 | + | Upstream | 5.56 | 3 |
47 | EVX2 | Even-skipped homeobox 2 | Chr2: 176653080 to 176656936 | - | Intragenic | 5.55 | 3 |
48 | AX747981 | Hypothetical gene | Chr8: 96148213 to 96154324 | - | Upstream | 5.48 | 3 |
49 | ST8SIA3 | St8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3 | Chr18: 53170718 to 53187159 | + | Intragenic | 5.47 | 3 |
50 | WT1 | Wilms tumor 1 | Chr11: 32365900 to 32413663 | - | Intragenic | 5.40 | 3 |
51 | BARHL2 | Barh-like homeobox 2 | Chr1: 90950167 to 90955382 | - | Upstream | 5.39 | 3 |
52 | IRX1 | Iroquois homeobox 1 | Chr5: 3649167 to 3654517 | + | Intragenic | 5.39 | 3 |
53 | KLF11 | Kruppel-like factor 11 | Chr2: 10101132 to 10112414 | + | Upstream | 5.26 | 3 |
54 | HLXB9 | Homeobox Hb9 | Chr7: 156479507 to 156496108 | - | Upstream | 5.25 | 3 |
55 | NKX2-8 | Nk2 homeobox 8 | Chr14: 36118966 to 36121537 | - | Upstream | 5.20 | 3 |
56 | ZFP91 | Zinc finger protein 91 homolog (mouse) | Chr11: 58103162 to 58145091 | + | Upstream | 5.07 | 3 |
57 | LHX2 | Lim homeobox 2 | Chr9: 125813709 to 125835263 | + | Intragenic | 5.04 | 3 |
58 | MEIS1 | Meis homeobox 1 | Chr2: 66516036 to 66653085 | + | Downstream | 5.00 | 3 |
59* | PAX2 | Paired box 2 | Chr10: 102495457 to 102579688 | + | Intragenic | 4.95 | 3 |
60* | LHX9 | Lim homeobox 9 | Chr1: 196153139 to 196165896 | + | Intragenic | 4.81 | 3 |
61 | GRASP | Grp1-associated scaffold protein | Chr12: 50687014 to 50695938 | + | Upstream | 4.78 | 3 |
62 | LHX8 | Lim homeobox 8 | Chr1: 75366706 to 75399806 | + | Intragenic | 4.77 | 3 |
63 | HOXD12 | Homeobox D12 | Chr2: 176672775 to 176673734 | + | Upstream | 4.66 | 3 |
64 | PAX5 | Paired box 5 | Chr9: 36828530 to 37024476 | - | Intragenic | 4.56 | 3 |
65 | LBX1 | Ladybird homeobox 1 | Chr10: 102976722 to 102978707 | - | Downstream | 4.53 | 3 |
66 | EGFR | Epidermal growth factor receptor | Chr7: 55054218 to 55242525 | + | Upstream | 4.45 | 3 |
67 | ODZ3 | Odz, odd Oz/ten-m homolog 3 | Chr4: 183302134 to 183508463 | + | Upstream | 4.40 | 3 |
68 | TM7SF4 | Transmembrane 7 superfamily member 4 | Chr8: 105421230 to 105438092 | + | Upstream | 4.22 | 3 |
69 | ZNF311 | Zinc finger protein 311 | Chr6: 29070573 to 29081014 | - | Downstream | 4.09 | 3 |
70 | PCDH19 | Protocadherin 19 | Chrx: 99433297 to 99551927 | - | Intragenic | 4.06 | 3 |
71 | FLJ45983 | Hypothetical gene | Chr10: 8132418 to 8135453 | - | Upstream | 3.84 | 3 |
72 | AX747375 | Hypothetical gene | Chr19: 41955897 to 41958529 | + | Downstream | 3.83 | 3 |
73 | PPP2R2C | Protein phosphatase 2 regulatory subunit B, gamma isoform | Chr4: 6373205 to 6525227 | - | Intragenic | 3.58 | 3 |
74 | EMX1 | Empty spiracles homeobox 1 | Chr2: 72998111 to 73015528 | + | Intragenic | 3.57 | 3 |
75 | PRKCSH | Protein kinase C substrate 80K-H | Chr19: 11407268 to 11422782 | + | Upstream | 3.56 | 3 |
76 | FZD1 | Frizzled homolog 1 | Chr7: 90731718 to 90736068 | + | Intragenic | 3.52 | 3 |
77 | LBX2 | Ladybird homeobox 2 | Chr2: 74578151 to 74583951 | - | Upstream | 3.42 | 3 |
78 | HOXC13 | Homeobox C13 | Chr12: 52618842 to 52626595 | + | Intragenic | 3.40 | 3 |
79 | MT1A | Metallothionein 1A | Chr16: 55230078 to 55231500 | + | Upstream | 3.36 | 3 |
80 | DLX5 | Distal-less homeobox 5 | Chr7: 96487637 to 96492079 | - | Intragenic | 3.06 | 3 |
81 | LDOC1L | Leucine zipper, downregulated in cancer 1-like | Chr22: 43267113 to 43272669 | - | Intragenic | 2.30 | 3 |