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Live Examples of what types of visualizations and analyses you can perform using UCSC Xena

Workshop cheatsheet/handout

Xena_Workshop_handout.pdf
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Xena Workshop Handout
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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).‌
Mathelier A, Lefebvre C, Zhang AW, Arenillas DJ, Ding J, Wasserman WW, Shah SP. Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas Genome Biology. 2015; 16:84.
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Workshop cheatsheet/handout
FOXM1a, FOXM1b, FOXM1c transcript expression in tumor vs. normal samples
PDL1 and PD1 expression across 39 cancer types in TCGA and TARGET
MGMT gene expression ~ promoter DNA methylation in GBM
ERG-TMPRSS2 fusion in prostate cancer
KM plot of breast cancer PAM50 subtypes
Genetic separation of lower grade gliomas: one characterized by loss of chromosomes 1p & 19q, the other by TP53 & ATRX mutations
Copy number for EGFR, PTEN, chromosome 1, 7, 10, 19 in TCGA brain tumors
Mutation pile-ups in intron enhancers in ICGC lymphoma
Stemness scores across TCGA cancer types