Table 3.
Tumor phenotypes and clinical parameters associated with t-SNE clustering
| Feature | Cluster | Comparison | P-value |
|---|---|---|---|
| Breast cancer | |||
| Her2/Neu status | Cluster 1–88.2% | Other tumors – 7.7% | < 0.0001 |
| Hepatocellular carcinoma | |||
| Hepatitis B | Cluster 2–38.4% | Other tumors – 18.6% | < 0.0001 |
| Endometrial carcinoma | |||
| Type II (serous) type | Cluster 1–32.4% | Other tumors – 5.2% | < 0.0001 |
| Locoregional disease or recurrence | Cluster 1–8.6% | Other tumors – 2.2% | 0.004 |
| Lung cancer | |||
| Adenocarcinoma | Cluster 2–80.0% | Other tumors – 37.8% | < 0.0001 |
| Squamous cell carcinoma | Cluster 4–73.6% | Other tumors – 34.2% | < 0.0001 |
| Kidney clear cell carcinoma | |||
| Gender | Cluster 1–92.9% female | Other tumors – 29.0% female | |
| Longest dimension | Cluster 2–1.5 cm | Other tumors – 1.8 cm | < 0.0001 |
| Histologic grade 3 or 4 | Cluster 3–69.0% | Other tumors – 41.5% | < 0.0001 |
| Pathologic stage III or IV | Cluster 3–58.5% | Other tumors – 25.5% | < 0.0001 |
| Thyroid carcinoma | |||
| Gender | Cluster 3–35.4% male | Other tumors – 11.3% male | < 0.0001 |
| Tall cell subtype | Cluster 1–17.2% | Other tumors – 5.03% | 0.0001 |
| Follicular subtype | Cluster 3–27.7% | Other tumors – 10.5% | < 0.0001 |
| Acute myeloid leukemia | |||
| Gender | Cluster 1–100% female Cluster 3–81.5% male |
Cluster 2–53.6% female | < 0.0001 |
| Complex (> 3 distinct) cytogenetic abnormalities | Cluster 3–21.0% | Other tumors – 5.5% | 0.0025 |
| Testicular cancer | |||
| Seminoma subtype | Cluster 1–100% | Other tumors – 14.5% | < 0.0001 |
| Embryonal carcinoma subtype | Cluster 2–94.6% | Other tumors – 20.6% | < 0.0001 |
| Teratoma subtype | Cluster 3–84.0% | Other tumors – 14.7% | < 0.0001 |
| Head and neck cancer | |||
| HPV infection | Cluster 1–46.1% | Other tumors – 9.8% | 0.0001 |
| Skin cutaneous melanoma | |||
| Breslow depth | Cluster 1–4.8 cm | Other tumors – 7.6 cm | 0.0083 |
| Brain cancer | |||
| Glioblastoma | Cluster 3–100% | Other tumors – 0% | < 0.0001 |
| Astrocytoma low-grade glioma | Cluster 2–53.0% Cluster 4–62.7% |
Other tumors – 2.5% | < 0.0001 |
| Non-astrocytoma low-grade glioma | Cluster 1–86.7% Cluster 5–97.0% |
Other tumors – 29.1% | < 0.0001 |
Tumor phenotypes and clinical markers were compared between tumor clusters using chi-squared tests, with significance defined as α < 0.01. “Other tumors” are comprised of all tumors from the same cancer cohort not falling into the given cluster. Data were obtained using the UCSC Xenabrowser, under the data heading “Phenotypes.” Cancer cohorts with no tumor clusters significantly associating with any clinical parameter were excluded from this table