Table 1.
Potential marker CpG sites discriminating the early recurrence (ER) group from the non-ER group based on Infinium assay, for which data had been verified using pyrosequencing in the initial cohort
| Probe IDa | Chromosome | Gene symbolb | CpG typec | Gene regiond |
|---|---|---|---|---|
| cg00945409 | 10 | ZMIZ1-AS1 | S_Shelf | Gene body |
| cg07846168 | 13 | GPC6 | Open sea | Gene body |
| cg17206555 | 7 | CDK14 | S_Shore | First intron |
| cg02046247 | 12 | NA | Open sea | Intergenic region |
| cg18289710 | 11 | PDGFD | Open sea | Gene body |
| cg09229620 | 3 | NLGN1 | S_Shore | 5′ UTR |
| cg15930703 | 2 | DOCK10 | Open sea | Gene body |
| cg21867733 | 12 | NCOR2 | Open sea | 5′ UTR |
| cg21873275 | 1 | NBPF25P | Open sea | Gene body |
| cg02192855 | 6 | HIST1H2BI | N_Shore | TSS200 |
| cg19918599 | 3 | NA | Open sea | Intergenic region |
| cg20549290 | 7 | GIMAP4 | Open sea | TSS1500 |
| cg14064694 | 6 | HIST1H2BI | Island | First exon |
| cg02627240 | 7 | TPK1 | Open sea | Gene body |
aProbe IDs for the Infinium HumanMethylation450 BeadChip (Illumina)
bNA: not annotated (located within intergenic regions)
cCpG islands, island shores (2000-bp regions adjacent to a CpG island), and island shelves (2000-bp regions adjacent to an island shore) are identified based on the University of California, Santa Cruz (UCSC) genome browser (https://genome.ucsc.edu/)
dTSS1500 (from 200 bp upstream of the transcription start site [TSS] to 1500 bp upstream of it), TSS200 (from TSS to 200 bp upstream of it), 5′ UTR (untranslated region), first exon, first intron, and gene body (second exon and downstream) are identified based on the RefSeq database (http://www.ncbi.nlm.nih.gov/refseq/)