Table 3.
Major RNA sequencing and DNA methylation features for NSCLC prediction.
| Ensemble Gene ID | Gene Symbol | Log2 Fold Change | Chromosome | GRCh38, Start | GRCh38, End | Length | Strand | Gene Type | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000171564 | FGB | 8.861 | 4 | 154,563,011 | 154,572,807 | 9796 | + | Protein coding | ||||||
| ENSG00000110680 | CALCA | 8.266 | 11 | 14,966,668 | 14,972,351 | 5683 | - | Protein coding | ||||||
| ENSG00000164266 | SPINK1 | 6.680 | 5 | 147,824,572 | 147,831,671 | 7099 | - | Protein coding | ||||||
| ENSG00000169469 | SPRR1B | 5.858 | 1 | 153,031,203 | 153,032,900 | 1697 | + | Protein coding | ||||||
| ENSG00000176153 | GPX2 | 5.854 | 14 | 64,939,152 | 64,942,905 | 3753 | - | Protein coding | ||||||
| ENSG00000167656 | LY6D | 5.698 | 8 | 142,784,882 | 142,786,539 | 1657 | - | Protein coding | ||||||
| ENSG00000143320 | CRABP2 | 5.559 | 1 | 156,699,606 | 156,705,816 | 6210 | - | Protein coding | ||||||
| ENSG00000205420 | KRT6A | 5.473 | 12 | 52,487,176 | 52,493,257 | 6081 | - | Protein coding | ||||||
| ENSG00000099953 | MMP11 | 5.135 | 22 | 23,768,226 | 23,784,316 | 16,090 | + | Protein coding | ||||||
| ENSG00000196611 | MMP1 | 5.042 | 11 | 102,789,401 | 102,798,160 | 8759 | - | Protein coding | ||||||
| ENSG00000204305 | AGER | −5.001 | 6 | 32,180,968 | 32,184,322 | 3354 | - | Protein coding | ||||||
| ENSG00000168484 | SFTPC | −4.729 | 8 | 22,156,913 | 22,164,479 | 7566 | + | Protein coding | ||||||
| ENSG00000165197 | VEGFD | −3.585 | X | 15,345,596 | 15,384,413 | 38,817 | - | Protein coding | ||||||
| ENSG00000164530 | PI16 | −3.539 | 6 | 36,948,263 | 36,964,837 | 16,574 | + | Protein coding | ||||||
| ENSG00000133800 | LYVE1 | −3.304 | 11 | 10,556,966 | 10,611,689 | 54,723 | - | Protein coding | ||||||
| CpG site_ID | Abs. Diff. 1 | Methyl. Pattern | Chromosome | UCSC_RefGene_Name | UCSC_RefGene_Group | UCSC_CpG_Islands_Name 2 | ||||||||
| cg25774643 | 0.561 | Hypermethylation | 11 | SCT | TSS200 | chr11:626728-628037 | ||||||||
| cg03502002 | 0.464 | Hypermethylation | 18 | GALR1;GALR1 | 1stExon;5′UTR | chr18:74961556-74963822 | ||||||||
| cg22674699 | 0.532 | Hypermethylation | 2 | HOXD9 | 1stExon | chr2:176986424-176988291 | ||||||||
| cg18322569 | 0.495 | Hypermethylation | 1 | BARHL2;BARHL2 | 5′UTR;1stExon | chr1:91182509-91182857 | ||||||||
| cg19760241 | 0.501 | Hypermethylation | 17 | LHX1 | Body | chr17:35291899-35300875 | ||||||||
| cg20399616 | 0.474 | Hypermethylation | 12 | BCAT1 | Body | chr12:25055599-25056246 | ||||||||
| cg21472506 | 0.517 | Hypermethylation | 2 | OTX1 | 3′UTR | chr2:63283936-63284147 | ||||||||
| cg04415798 | 0.490 | Hypermethylation | 14 | PAX9 | 5′UTR | chr14:37126786-37128274 | ||||||||
| cg18077971 | 0.469 | Hypermethylation | 2 | PAX3 | TSS1500 | chr2:223162946-223163912 | ||||||||
| cg27071152 | 0.474 | Hypermethylation | 7 | LOC646999 | Body | chr7:39649253-39649510 | ||||||||
| cg07860213 | 0.486 | Hypermethylation | 8 | PRDM14 | Body | chr8:70981873-70984888 | ||||||||
| cg26799474 | 0.387 | Hypomethylation | 2 | CASP8 | 5′UTR | Not applicable | ||||||||
| cg25247520 | 0.432 | Hypomethylation | 8 | MIR1204;PVT1 | TSS200;Body | chr8:128806081-128806899 | ||||||||
| cg07551060 | 0.399 | Hypomethylation | 10 | GRK5 | Body | chr10:121075133-121075401 | ||||||||
| cg06051311 | 0.404 | Hypomethylation | 6 | TRIM15 | 5′UTR;1stExon | chr6:30130969-30131093 | ||||||||
1 Absolute differences in beta-value between cancer and non-cancer samples.2 CpG sites is based on the reference human genome (GRCh37/hg19) assembly.