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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
  1. aFor definitions of upstream, intragenic, and downstream, see Materials and methods (Microarray data analysis). The transcripts that have either upstream, intragenic or downstream peaks in at least three out of six DCIS samples were selected as positive targets. *Gene targets verified by combined bisulfite restriction analysis assays or bisulfite sequencing. bAverage of the log2 ratios assigned to positive peaks across the six DCIS. cHomeobox genes are indicated in bold.