Advanced Tutorial: Section 1

Learn how to view whole chromosomes and view advanced datasets such as exon expression

Description

This tutorial is made for those who have basic knowledge 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 basic knowledge of how to build and read a Visual Spreadsheet. To get this, go through Basic Tutorial: Section 1.

Estimated time needed

10 min‌

Learning goals

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

Tutorial

We will look at the ERG-TMPRSS2 gene fusion 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. TMPRSS2 is expressed at high levels in normal prostate tissue. This allows ERG to use the TMPRSS2 promoter to increase ERG expression.

​Ending Screenshot​

Note that column D may look slightly different, depending on how you resize and zoom the column.

We can now see that there are many patient's samples with relatively high expression of ERG (column B). 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 also have an intra-chromosomal 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. Start at https://xenabrowser.net/

  2. Type 'TCGA Prostate Cancer (PRAD)', select this study from the drop down menu, and click 'To first variable'.

  3. Type 'ERG', select the checkbox for Gene Expression and click 'To second variable'.

  4. Type 'ERG', click 'Show Advanced', select the checkbox for 'IlluminaHiSeq' under 'exon expression RNAseq', and click 'Done'.

  5. Click the text 'Click to insert a column' after column C. Type 'chr21', select the checkbox for Copy Number and click 'Done'.

  6. Click on the filter menu and select 'Remove samples with nulls'

  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. 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

Add copy number data for chromosome 1.

Add DNA Methylation data for ERG.

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