Xena is the latest cancer genome visualization software being developed by Mary Goldman at UCSC Genomics Institute. The following examples demonstrate the functionality delivered by this software.
Cancer cells have many ways of evading apoptosis. Mutating P53, a tumor suppressor gene or upregulating expression of telomerase are just a couple.
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Explore telomerase pathway genes in TCGA Low Grade Glioma (LGG)
EGFR DNA amplification is a common molecular abnormality in glioblastoma.
PTEN is also an important tumor suppressor which is found to be mutated in many human cancers.
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Observe copy number variations in TCGA brain tumors
FOXM1 is involved in the regulation of cell cycle.
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Transcript expression in tumor vs. normal samples
Molecular signatures from gene sets (PAM50) are used to classify breast cancer subtypes. Within a subtype, the cancer cells often respond more similarly to particular treatments.
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Overall survival of breast cancer patients
Specific regions of the genome are more susceptible to breaks, mutations or methylation. These regions can vary by tissue type, cancer type.
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Mutation pile-ups in intron enhancers in ICGC lymphoma
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Gene expression across 39 cancer types in TCGA and TARGET
Gene fusions have been challenging to detect, verify, and visualize.
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Gene fusions and deletions in prostate cancer
Chromosome 1p, 19q interaction has been studied for more than 40 years, (Schober AM Fonatsch C. Balanced reciprocal whole-arm translocation t(1;19) in three generations. Hum Genet 1978;42:349–52)
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Co-deletion of chromosomes in TCGA lower grade gliomas
Now it's your turn! Try to investigate the gene: CDKN2A copy number variation in the project: TCGA, cancer: LGG. It is often deleted, either homozygous or heterozygously.