Table 4.
Average TPM of coding and non-coding genes in the LD blocks of the most significant GWAS markers calculated for each bladder cancer cell line.
| Marker | Coding and non-coding genes | Control tissue | Bladder Ca | Transit. cell Ca | Squamous cell Ca | Ur. urothelial Ca | Mus. Inv. Urothelial Ca |
|---|---|---|---|---|---|---|---|
| rs1924557 | LPHN2 | 6.87 | 17.47 | 24.25 | 11.00 | 5.00 | 1.32 |
| rs4745 | EFNA1 | 8.25 | 31.30 | 78.50 | 20.00 | 7.00 | 4.06 |
| rs4745 | SLC50A1 | 0.24 | 62.60 | 46.00 | 26.00 | 46.00 | 4.15 |
| rs4745 | DPM3 | 131.29 | 66.55 | 82.50 | 16.00 | 79.00 | 4.77 |
| rs4745 | KRTCAP2 | 170.89 | 18.95 | 15.75 | 10.00 | 16.00 | 11.37 |
| rs6874700 | ISL1 | 0.36 | 0.61 | 2.03 | 3.00 | 0.00 | 0.06 |
| 11:119964758 | TRIM29 | 11.86 | 52.27 | 61.25 | 19.00 | 0.20 | 5.15 |
| rs10862001 | SYT1 | 0.06 | 4.30 | 8.13 | 4.00 | 0.40 | 1.05 |
| rs10862001 | PAWR | 13.47 | 37.65 | 49.25 | 12.00 | 22.00 | 5.46 |
| rs10853087 | GOSR2 | 11.25 | 16.80 | 12.50 | 5.00 | 16.00 | 3.69 |
| rs6874700 | HMGB1P47 | RNA-polyA-seq | 0.00 | 0.00 | 0.00 | 0.00 | RNA-polyA-seq |
| rs6874700 | ISL1-DT | RNA-polyA-seq | 0.11 | 0.20 | 0.5 | 0.00 | RNA-polyA-seq |
| rs10853087 | LINC01974 | RNA-polyA-seq | 0.04 | 0.00 | 0.00 | 0.00 | RNA-polyA-seq |
| 20:55165923 | LINC01716 | RNA-polyA-seq | 0.01 | 0.00 | 0.00 | 0.00 | RNA-polyA-seq |
urothelial carcinoma tissues and control bladder tissue.
TPM for Non-coding genes in Control tissue and Muscolar invasive urothelial cancer do not show reads due to polyA-sequencing. Legend: Bladder tissue of a 3-year-old bladder donor (control tissue); Bladder carcinoma (Bladder Ca); Bladder transitional cell carcinoma (Transit. cell Ca); Bladder squamous cell carcinoma (Squamous Ca); Ureter urothelial carcinoma (Urothelial Ca); Bladder urothelial carcinoma (Bl. urothelial Ca); Muscle invasive urothelial cancer (Mus. Inv. Urothelial Ca); RNA-polyA-seq data do not include miRNAs or lincRNAs.