---
description: >-
  Live Examples of what types of visualizations and analyses you can perform
  using UCSC Xena
---

# Live examples

## Workshop cheatsheet/handout

{% file src="https://3676322134-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LAsF1Wuj3-Bs3YBFd7f%2F-Lv7UIn_8KHw9kJFMjK8%2F-Lv7Uaexc8-rGLEO-S4x%2FXena_Workshop_handout.pdf?alt=media&token=4e6eb94a-0a6f-4452-880d-1185ad422837" %}
Xena Workshop Handout
{% endfile %}

## [FOXM1a, FOXM1b, FOXM1c transcript expression in tumor vs. normal samples](https://xenabrowser.net/heatmap/?bookmark=634da50313613e659e865c2bfb958ea1)

![https://xenabrowser.net/heatmap/?bookmark=634da50313613e659e865c2bfb958ea1](https://3676322134-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LAsF1Wuj3-Bs3YBFd7f%2F-Lzn2eYWs0YfpZZFXF30%2F-LznB-DMJba0jFel6LAO%2FScreen%20Shot%202020-01-29%20at%2012.42.55%20PM.png?alt=media\&token=1a11f39a-5d96-4d8d-a8fc-d08c26ac2ed8)

## [PDL1 and PD1 expression across 39 cancer types in TCGA and TARGET](https://xenabrowser.net/?bookmark=16e1d1a37ab7d9820a6bf1399ce5135e)

![https://xenabrowser.net/?bookmark=16e1d1a37ab7d9820a6bf1399ce5135e](https://3676322134-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LAsF1Wuj3-Bs3YBFd7f%2F-LznBLz7s1osAFOex-9V%2F-LznBjpgzeJ57n_v8D70%2FScreen%20Shot%202020-01-29%20at%201.26.28%20PM.png?alt=media\&token=0cf9f75f-82f0-4b4e-af60-5bf12b6116fe)



## [MGMT gene expression \~ promoter DNA methylation in GBM](https://xenabrowser.net/heatmap/?bookmark=3547cb283a111e68991e9b8a8d5f8b42)

![https://xenabrowser.net/?bookmark=048e461b1819bc84808edc16b34e974b](https://3676322134-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LAsF1Wuj3-Bs3YBFd7f%2F-L_F10Jm_qiP7hG35Nud%2F-L_F2Th5p85IQOK07P2T%2FDNA%20methylation-01.png?alt=media\&token=4fc12dcf-a05f-417b-ad4e-f4ad71a1ec6b)

## [ERG-TMPRSS2 fusion in prostate cancer](https://xenabrowser.net/heatmap/?bookmark=2e553fc5ca9858653e225fabce0c36ab)&#x20;

![https://xenabrowser.net/heatmap/?bookmark=2e553fc5ca9858653e225fabce0c36ab](https://3676322134-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LAsF1Wuj3-Bs3YBFd7f%2F-L_JyDULnFWJuXklB8ev%2F-L_JyIY4iaMcT3sgDsPu%2FFusion%20expression-01.png?alt=media\&token=63c7e9bf-2282-4d07-91c6-44a432f986cf)

## [KM plot of breast cancer PAM50 subtypes](https://xenabrowser.net/heatmap/?bookmark=c03d52bed79d2b474ffcef679796a12d)

![https://xenabrowser.net/heatmap/?bookmark=c03d52bed79d2b474ffcef679796a12d](https://3676322134-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LAsF1Wuj3-Bs3YBFd7f%2F-L_F73gViKH9zjLOXueo%2F-L_F77cT9NqbYBhvN1B9%2FxenaDownload-01.png?alt=media\&token=346e831e-f9b8-4cf9-b5b0-9f33fcf08cbb)

## [Genetic separation of lower grade gliomas: one characterized by loss of chromosomes 1p & 19q, the other by TP53 & ATRX mutations](https://xenabrowser.net/heatmap/?bookmark=d5de509a8ff0032298a0547c97638e3f)

![https://xenabrowser.net/heatmap/?bookmark=d5de509a8ff0032298a0547c97638e3f](https://3676322134-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-LAsF1Wuj3-Bs3YBFd7f%2Fuploads%2FBkoex52f4MC6ACLbj3C1%2FScreenshot%202024-12-19%20at%2011.32.52%E2%80%AFAM.png?alt=media\&token=18a6e0c2-84ce-4266-839e-3289c6eba4f9)

## [Copy number for EGFR, PTEN, chromosome 1, 7, 10, 19 in TCGA brain tumors](https://xenabrowser.net/heatmap/?bookmark=c6429007551de3bf0ea491c96814a1cf)

![https://xenabrowser.net/heatmap/?bookmark=c6429007551de3bf0ea491c96814a1cf](https://3676322134-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LAsF1Wuj3-Bs3YBFd7f%2F-LznBn5w9kVOq3wVrWqN%2F-LznCG0NNg2Nz-XV7att%2FScreen%20Shot%202020-01-29%20at%201.28.46%20PM.png?alt=media\&token=3531df01-3100-4136-9091-d63273858b3a)

## [Mutation pile-ups in intron enhancers in ICGC lymphoma](https://xenabrowser.net/heatmap/?bookmark=ba5edb23fe570ef22f5f518859ca0911)

![https://xenabrowser.net/heatmap/?bookmark=ba5edb23fe570ef22f5f518859ca0911](https://3676322134-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LAsF1Wuj3-Bs3YBFd7f%2F-LaHXsbz0H0wAV_ToMaQ%2F-LaHZso11OMztp0SagEG%2FicgcIntronMutation.png?alt=media\&token=053c195f-873f-402e-a085-fd93c50aee73)

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" %}

## [Stemness scores across TCGA cancer types](https://xenabrowser.net/?bookmark=046e741291000b1b366c70ec5a3cd39f)

![https://xenabrowser.net/?bookmark=046e741291000b1b366c70ec5a3cd39f](https://3676322134-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LAsF1Wuj3-Bs3YBFd7f%2F-L_FDEU1_NPuffLPljkP%2F-L_FDIpl3Ciy25GCMXeE%2FSFigure%205%20stemness.png?alt=media\&token=9711caf6-5bc6-4f80-9aa3-1cd801c9b48e)
