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Advanced Tutorial: Section 1
Learn how to view whole chromosomes and view advanced datasets such as exon expression

Description

This tutorial is intended for those who have a basic understanding of how to use Xena. We will cover how to view whole chromosome and how to use the advanced dataset menu to access datasets such as exon expression.

Prerequisites

This tutorial assumes a basic understanding of how to build and read a Visual Spreadsheet. This can be achieved through completion of the Basic Tutorials, especially the Basic Tutorial: Section 1.

Estimated time needed

10 min‌

Learning goals

Create a visual spreadsheet that include a chromosome-wide column and data from the advanced dataset menu

Tutorial

We will investigate the ERG-TMPRSS2 gene fusion and TMPRSS2 promoter hijacking in patients from the TCGA Prostate Cancer study.
ERG is an oncogene that expressed at low levels in normal prostate tissue. Some patient's prostate cancer samples have higher expression of ERG. These samples tend to have an intra-chromosomal deletion that fuses ERG to TMPRSS2. As TMPRSS2 is expressed at high levels in normal prostate tissue, this allows ERG to hijack the TMPRSS2 promoter which leads to increased ERG expression.
Note that column D may look slight different, depending on how resize and zoom the column.
We can now see that there are many patient's samples with relatively high expression of ERG (column B), and that if we look more closely that this relatively high expression is not uniform across the exons of ERG, but instead is in the exons closer to the 3' end of the gene (column C). Looking at column D, we can see that these samples that have relatively high expression also have an interchromosomal deletion of part of chromosome 21. If we hover over the genes at either end of the deletion, we can see that the end points fall within ERG and TMPRSS2.

Steps

  1. 1.
    Start at https://xenabrowser.net/​
  2. 2.
    Type 'TCGA Prostate Cancer (PRAD)', select this study from the drop down menu, and click 'Done'.
  3. 3.
    Type 'ERG', select the checkbox for Gene Expression and click 'Done'.
  4. 4.
    Type 'ERG', click 'Show Advanced', select the checkbox for 'IlluminaHiSeq' under 'exon expression RNAseq', and click 'Done'.
  5. 5.
    Click the text 'Click to insert a column' after column C. Type 'chr21', select the checkbox for Copy Number and click 'Done'.
  6. 6.
    Click on the filter menu and select 'Remove samples with nulls'
  7. 7.
    Click on the handle in the lower right corner of column E, copy number for chromosome 21. Move it to the right to make the column bigger.
  8. 8.
    Click and drag within column E, copy number for chromosome 21 to zoom into the intra-chromosomal deletion.

Video of steps 1-4

‌Video of steps 5-8

More information:

Test your knowledge

Question 1
Answer 1
Add copy number data for chromosome 1.
​Ending Screenshot​
Question 2
Answer 2
Add DNA Methylation data for ERG.
​Ending Screenshot​
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Description
Prerequisites
Estimated time needed
Learning goals
Tutorial
Test your knowledge