Table 2.
Overview of the Illumina CpG sites that were used in the final prediction models for both pan‐cancer and type‐specific classification. IGR, intergenomic region; TSS, transcription start site; UTR, untranslated region.
| Probe ID | Chromosome | Strand | Gene | Genomic feature | Relation to CpG Island |
|---|---|---|---|---|---|
| cg17757602 a | 5 | F | – | IGR | Island |
| cg26848718 a | 11 | R | WT1 | Body | Island |
| cg05422029 a | 6 | F | – | IGR | Open Sea |
| cg22749589 a | 20 | F | – | IGR | North Shore |
| cg02615833 b | 5 | R | PCDH24 | TSS200 | Open Sea |
| cg26175343 b | 20 | F | LRRN4 | TSS200 | South Shore |
| cg14266927 b | 14 | R | BATF | TSS1500 | Open Sea |
| cg16937769 b | 12 | R | HOXC4 | TSS1500 | South Shore |
| cg24750391 b | 7 | F | PON3 | TSS1500 | South Shore |
| cg23921838 b | 6 | F | C6orf97 | 3'UTR | Open Sea |
| cg21710324 b | 1 | F | TMEM63A | 5'UTR | North Shore |
| cg10588135 b | 17 | R | BCAS3 | Body | Open Sea |
| cg00851394 b | 19 | F | CNTD2 | Body | Island |
| cg22966302 b | 19 | F | NFIX | Body | North Shelf |
| cg00501869 b | 7 | R | PTPRN2 | Body | Island |
| cg23313005 b | 5 | F | FAM193B | Body | Open Sea |
| cg12126990 b | 2 | R | AFF3 | Body | Open Sea |
| cg24686845 b | 12 | F | PLXNC1 | Body | Open Sea |
| cg10210594 b | 1 | F | – | IGR | Island |
| cg11518509 b | 1 | R | – | IGR | Open Sea |
| cg19251600 b | 6 | F | – | IGR | Open Sea |
| cg16196175 b | 7 | F | – | IGR | North Shore |
| cg21312554 b | 8 | R | – | IGR | Open Sea |
| cg27628707 b | 15 | R | – | IGR | Open Sea |
a
Denotes pan‐cancer CpG markers.
b
Denotes type‐specific CPG markers.