Basic Tutorial: Section 1

Learn to create your first views in Xena

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.

Link to Ending Screenshot

Steps

Start at our home page http://xena.ucsc.edu/ and click on 'Launch Xena'. You are now in our Visual Spreadsheet Wizard.
Type 'GDC TCGA Lung Adenocarcinoma (LUAD)', select this study from the drop down menu, and click 'To first variable'.
Type 'EGFR', select the checkboxes for Gene Expression, Copy Number, and Somatic Mutation, and click 'To second variable'.

Video of steps:

How to read a Visual Spreadsheet

Samples are on the y-axis and your columns of data are on the x-axis. We line up columns so that each row is the same sample, allowing you to easily see trends in the data. Data is always sorted left to right and sub-sorted on columns thereafter.

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).

More information

Making your own Visual Spreadsheet: Which TCGA study to choose

There are 4 versions of the TCGA data in Xena. In this example we selected the TCGA data from the GDC. This page can help you decide which version of TCGA data to use for your own analysis.

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

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.
Resize columns. Click the handle in the lower right corner of column D, mutation. Move it to the right to make the column bigger.
Zoom in on a column. Click and drag within column D. Release to zoom.
Zoom out on a column. Click the red zoom out text at the top of column D.
Zoom in on samples. Click and drag vertically in any column in the Visual Spreadsheet to zoom in on these samples.
Zoom out on samples. To zoom out click either 'Zoom out' or 'Clear zoom' at the top of the Visual Spreadsheet.