Table 1 Summary of 17 DMRs associated with overall survival in TCGA TNBC.
Chr | Start | End | RefSeq Location | CpG island | CpG shore | Dnase hypersensitive site | Conserved transcription factor binding sites ( Z score cutoff=2.33) | ChromHMM HMEC polycomb | Prognostic probes | Gene function/location |
|---|---|---|---|---|---|---|---|---|---|---|
Poor prognosis | ||||||||||
 chr1 | 50,658,646 | 50,659,783 | DMRTA2* | Yes | No | Yes | GRα | Yes | 3 | Doublesex- and Mab-3-related transcription factor |
 chr1 | 75,368,128 | 75,368,976 | LHX8* | Yes | Yes | Yes | NA | Yes | 3 | Homeobox protein Lhx8 |
 chr10 | 102,409,068 | 102,409,766 |  | Yes | Yes | No | STAT1β, NK-κB, CREB, NF-Y, CEBPα | Yes | 5 | Intergenic region, ChromHMM polycomb marked |
 chr11 | 32,404,535 | 32,407,465 | WT1* | Yes | Yes | Yes | EGR1, EGR2, EGR2, NF1, LMO2, RFX1, MIF1, CREB, cJUN, ATF, ATF2 | Yes | 5 | Wilms tumour protein, transcription factor |
 chr11 | 32,416,010 | 32,417,947 | WT1-AS* | Yes | Yes | Yes | NA | Yes | 4 | Wilms tumour protein, antisense transcipt |
 chr13 | 27,398,788 | 27,401,867 |  | Yes | Yes | Yes | NA | Yes | 4 | Intergenic region, ChromHMM polycomb marked |
 chr14 | 56,330,541 | 56,332,135 |  | Yes | Yes | Yes | USF1, MAX1, c-MYC | Yes | 3 | Intergenic region, ChrommHMM polycomb |
 chr17 | 44,159,065 | 44,159,578 | HOXB13* | Yes | Yes | Yes | HSF1, HSF2 | Yes | 3 | Homeobox gene family, transcription factor |
 chr2 | 233,058,433 | 233,060,592 | ECEL1* | Yes | Yes | Yes | NRSF, PAX2, STAT5A, YY1, AHR, GATA2, AP2 | Yes | 3 | Zinc-containing typeII integral-membrane protein |
 chr3 | 182,923,564 | 182,924,686 | SOX2-OT* | No | No | Yes | NA | Yes | 4 | Non-protein coding RNA gene |
 chr5 | 1,498,811 | 1,499,696 | SLC6A3†| Yes | Yes | Yes | NA | Yes | 3 | Neurotransmitter reporter |
 chr6 | 27,620,848 | 27,621,582 |  | No | No | Yes | NA | No | 3 | ChromHMM promoter marked, Intergenic region |
 chr6 | 127,881,341 | 127,882,455 | C6orf174*†| No | Yes | Yes | STAT5A, FOXC1 | Yes | 6 | Chromosome 6 open reading frame SOGA3 protein coding region |
 chr7 | 121,726,837 | 121,728,266 |  | Yes | Yes | Yes | CHX10 | Yes | 4 | ChromHMM polycomb marked |
Good prognosis | ||||||||||
 chr11 | 32,413,697 | 32,415,714 | WT1/WT1-AS†| Yes | Yes | Yes | E47, AP4, c-MYC, ARNT | Yes | 5 | Bi-directional promoter of WT1/WT1-AS transcription factor |
 chr19 | 24,061,637 | 24,062,272 | ZNF254*†| No | No | Yes | NA | No | 4 | Zinc finger protein,transcriptional regulation |
 chr22 | 44,641,414 | 44,642,542 |  | Yes | Yes | Yes | NA | Yes | 3 | Intergenic region, ChromHMM promoter |
