Table 5.
log2-fold change of genes in the LD blocks of the most significant GWAS markers of bladder cancer cell types and muscle-invasive urothelial cancer over bladder control tissue.
| Marker | Coding and non-coding genes | Control tissue vs. bladder Ca | Control tissue vs. transit. cell Ca | Control tissue vs. squamous cell Ca | Control tissue vs. Ur. urothelial Ca | Control tissue vs. Mus. Inv. urothelial Ca |
|---|---|---|---|---|---|---|
| rs1924557 | LPHN2 | 1.35 | 1.82 | 0.68 | 0.46 | −2.38 |
| rs4745 | EFNA1 | 1.92 | 3.25 | 1.28 | −0.24 | −1.02 |
| rs4745 | SLC50A1 | 8.03 | 7.58 | 6.76 | 7.58 | 4.11 |
| rs4745 | DPM3 | −0.98 | −0.67 | −3.04 | −0.73 | −4.78 |
| Rs4745 | KRTCAP2 | −3.17 | −3.44 | −4.09 | −3.42 | −3.91 |
| rs6874700 | ISL1 | 0.75 | 2.49 | 3.06 | suppressed | −2.70 |
| 11:119964758 | TRIM29 | 2.14 | 2.37 | 0.68 | −5.89 | −1.20 |
| rs10862001 | SYT1 | 6.16 | 7.08 | 6.06 | 2.74 | 4.13 |
| rs10862001 | PAWR | 1.48 | 1.87 | −0.17 | 0.71 | −1.30 |
| rs10853087 | GOSR2 | 0.54 | 0.12 | −1.21 | −0.47 | −1.65 |
| rs6874700 | HMGB1P47 | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq |
| rs6874700 | ISL1-DT | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq |
| rs10853087 | LINC01974 | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq |
| 20:55165923 | LINC01716 | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq | RNA-polyA-seq |
Bold: differential expressed genes (log2fc <−1.5 or >1.5)
Log2 fold change for non-coding genes of different bladder cancers and Muscolar Invasive Urothelial cancer over control tissue shows no value due to polyA-sequencing of control tissue. Differential Expression defined with log2fc <−1.5 or >1.5 (marker in bold italic letters). 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 does not include miRNAs or lincRNAs). log2fc log2 fold change; differential expression defined with log2fc <−1.5 or >1.5 (marker in bold italic letters). vs. versus, Chr. chromosome.