User Help Pages
  • Welcome to the Help Pages for UCSC Xena
  • Tutorials and webinars
    • Webinars
    • Basic Tutorial: Section 1
    • Basic Tutorial: Section 2
    • Basic Tutorial: Section 3
    • Advanced Tutorial: Section 1
    • Advanced Tutorial: Section 2
    • Tutorial: Tumor vs Normal
    • Tutorial: Viewing your own data
    • Live examples
  • How do I ...
    • How do I make a KM plot?
    • How do I compare tumor vs normal expression?
    • How do I remove null data (gray lines) from view?
    • How do I make subgroups?
    • How do I make more than 2 subgroups?
    • How do I make subgroups with geneA high and geneB high?
    • How do I compare gene expression between subgroups?
    • How do I compare gene expression between different cancer types?
    • How do I remove duplicate samples from a KM plot?
    • How do I view multiple types of cancer together?
    • How do I filter to just one cancer type
    • How do I view my data with the data from TCGA?
    • How do I change the color of a column?
    • How do I interact with the tooltip?
    • How do I cite UCSC Xena?
  • Overview of features
    • Visual Spreadsheet
      • Coloring for Mutation Columns
      • Coloring for Segmented Copy Number Columns
    • Kaplan Meier Plots
    • Chart & Statistics View
    • Filtering and subgrouping
      • Supported search terms for finding samples
    • Differential Gene Expression
    • GSEA
    • Genomic Signatures
    • Bookmarks
    • Download Data
    • Xena Single Cell
    • TumorMap
    • MuPIT
    • Accessing data through python
    • Transcript View
    • Xena Gene Set Viewer
  • Overview of public data
    • Types of data we have
    • TCGA
    • GDC
    • More studies
    • Choosing a study/cohort
  • FAQ
    • Xena Browser
    • Data and datasets
  • Viewing your own data
    • Getting Started
    • Probes/transcripts/identifiers we recognize
    • Data format specifications and supported biological data types
    • KM plots using data from a Local Xena Hub
    • Hubs for institutions, collaborations, labs, and larger projects
    • Loading data from the command line
    • FAQ/Troubleshooting Guide
  • Technical documentation
    • Setting up Xena for your institution
    • Deep Linking Into Xena
    • Metadata Specification
  • Contact us
  • Cite us
  • Data Use Agreement
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On this page
  • 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

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  1. Tutorials and webinars

Live examples

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

Last updated 4 months ago

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Workshop cheatsheet/handout

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).‌

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
FOXM1a, FOXM1b, FOXM1c transcript expression in tumor vs. normal samples
LogoCis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas - Genome BiologyBioMed Central
328KB
Xena_Workshop_handout.pdf
pdf
Xena Workshop Handout
https://xenabrowser.net/heatmap/?bookmark=d5de509a8ff0032298a0547c97638e3f
https://xenabrowser.net/heatmap/?bookmark=634da50313613e659e865c2bfb958ea1
https://xenabrowser.net/?bookmark=16e1d1a37ab7d9820a6bf1399ce5135e
https://xenabrowser.net/?bookmark=048e461b1819bc84808edc16b34e974b
https://xenabrowser.net/heatmap/?bookmark=2e553fc5ca9858653e225fabce0c36ab
https://xenabrowser.net/heatmap/?bookmark=c03d52bed79d2b474ffcef679796a12d
https://xenabrowser.net/heatmap/?bookmark=c6429007551de3bf0ea491c96814a1cf
https://xenabrowser.net/heatmap/?bookmark=ba5edb23fe570ef22f5f518859ca0911
https://xenabrowser.net/?bookmark=046e741291000b1b366c70ec5a3cd39f