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Live Examples of what types of visualizations and analyses you can perform using UCSC Xena |
{% file src="../.gitbook/assets/xena_workshop_handout (1).pdf" %} Xena Workshop Handout {% endfile %}
Genetic separation of lower grade gliomas: one characterized by loss of chromosomes 1p & 19q, the other by TP53 & ATRX mutations
Xena mutation views supports examination of both coding and non-coding mutations from whole genome analysis. We support viewing mutations from both gene- or coordinate- centric perspective. In the gene-centric view, you can dynamically toggle to show or hide introns from the view. This figure shows the frequent intron mutations in 321 samples from the ICGC lymphoma cohorts. These 'pile-ups' would be not be visible if viewing mutations only in the exome. These intron mutations overlap with known enhancers regions (Mathelier 2015).
{% embed url="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0648-7" %}
