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Table 3 Tumor phenotypes and clinical parameters associated with t-SNE clustering

From: Diagnostic and prognostic implications of ribosomal protein transcript expression patterns in human cancers

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

  1. 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