Basic Step-by-Step Tutorial

Advanced Step-by-Step Tutorial

Video Tutorials

Overview of Xena (2 min)

Beginner Tutorial (17 min)

Advanced Tutorial (55 min)

Recording of tutorial given for NCI in May 2021. Includes closed captioning.

https://cbiit.webex.com/cbiit/lsr.php?RCID=acf4ea46dd9e41338662f0ba1ac59754

Workshop Cheatsheet/Handout

How do I ...

How do I ... guides are useful if you have a specific question.

Request a workshop

Workshops are a great way to teach a group of people how to use Xena. They can be 1-hour, 1/2-day, or 1-day in length. Currently we are only giving workshops remotely via Zoom or a similar technology. We give workshops both within the USA and internationally. Please contact us for more information: genome-cancer@soe.ucsc.edu

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​

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

Test your knowledge

Description

This tutorial is made for those who have never used Xena. We will cover how to create a Visual Spreadsheet with gene expression, mutation, and copy number variation data.

Prerequisites

This tutorial assumes basic knowledge of

• gene expression, copy number variation, and mutational genomic sequencing data

• how a change in copy number variation or mutations can lead to a change in gene expression

• The Cancer Genome Atlas (TCGA)

These resources can help you gain basic knowledge of these concepts:

Estimated time needed

Part A: 5 min

Part B: 10 min

Learning goals

Part A

• Create a Visual Spreadsheet

• Compare data across columns

Part B

• Move columns

• Resize columns

• Zoom in and out

Tutorial

We are going to look at EGFR aberrations in patients with lung adenocarcinomas using TCGA data. We will be looking at mutations and copy number aberrations and how they change gene expression.

Part A

Our goal is to build a Visual Spreadsheet and understand the relationship between the columns of data.

Steps

2. Type 'GDC TCGA Lung Adenocarcinoma (LUAD)', select this study from the drop down menu, and click 'To first variable'.

3. Type 'EGFR', select the checkboxes for Gene Expression, Copy Number, and Somatic Mutation, and click 'To second variable'.

Video of steps:

Biological interpretation

We can see that samples from TCGA patients that have high expression of EGFR (red, column B) tend to either have amplifications of EGFR (red, column C) or mutations in EGFR (blue tick marks, column D).

Part B

We will now move the columns to change the sort order and resize columns. We will zoom in to the whole Visual Spreadsheet and also within a column.

Steps

1. Move columns. Click column C, copy number variation, and drag it to the left so that it becomes the first column after the samples column (i.e. column B). Note that the samples are now sorted by the values in this column.

2. Resize columns. Click the handle in the lower right corner of column D, mutation. Move it to the right to make the column bigger.

3. Zoom in on a column. Click and drag within column D. Release to zoom.

4. Zoom out on a column. Click the red zoom out text at the top of column D.

5. Zoom in on samples. Click and drag vertically in any column in the Visual Spreadsheet to zoom in on these samples.

6. Zoom out on samples. To zoom out click either 'Zoom out' or 'Clear zoom' at the top of the Visual Spreadsheet.

Video of step 1

Video of step 2

Video of steps 3-6

Test your knowledge

Description

This tutorial is made for those who have never used Xena but who have completed Section 1 of the Basic Tutorial. We will cover how to filter to just the samples you are interested in, how to create subgroups, and how to run a Kaplan Meier survival analysis.

Prerequisites

This tutorial assumes completion of the . This tutorial begins where the Basic Tutorial: Section 1 ends.

Estimated time needed

Part A: 7 min

Part B: 15 min

Part C: 5 min

Learning goals

Part A

• Search for samples of interest

• Remove samples with no data

Part B

• Make subgroups

• Rename subgroups

Part C

• Run a Kaplan Meier survival analysis

• Use a custom time endpoint

Tutorial

In the Basic Tutorial Section 1 we found that we found that samples from patients that have aberrations in EGFR have relatively higher expression. These aberrations could be mutations or copy number amplifications.

Now we are going to look at whether those patient with aberrations in their samples also have a worse survival prognosis.

Part A

Our goal is to remove patient's samples with no data (i.e. null) from the view. This will make the view look cleaner and remove irrelevant samples from our Kaplan Meier survival analysis.

Steps

1. Type 'null' into the samples search bar. This will highlight samples that have 'null' values in any column on the screen. Null means that there is no data for that sample for that column.

2. Click the filter menu and select 'Remove samples'.

3. Delete the search term.

Video of steps

Shortcut for Part A

Instead of typing 'null' and removing those samples from the view, you can also use the 'Remove samples with nulls' shortcut in the filter menu.

Part B

Our goal is to create two subgroups, those patient's with samples with aberrations in EGFR and those patient's samples without aberrations in EGFR. We will then name the subgroups.

Steps

1. Type '(mis OR inframe) OR B:>0.5' into the samples search bar. This will select samples that either have a missense or inframe deletion '(mis OR inframe)', or where copy number variation (column B) is greater than 0.5. Note that I arbitrarily choose a cutoff of 0.5.

1. Click the filter menu and select 'New subgroup column'. This will create a new column that has samples that met our search term marked as 'true' (ie. those that have an EGFR aberration) and those that did not meet our search term as 'false' (ie. those that do not have an EGFR aberration).

2. Click the column menu for the column we just created (column B) and chose 'Display'.

3. Rename the display so that samples that are 'true' are instead labeled as 'EGFR Aberrations' and the samples that are 'false' are instead labeled as 'No EGFR Aberrations'. Click 'Done'

4. Delete the search term. This will remove the black tick marks for matching samples.

Video of steps 1