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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.

Steps

  1. 1.
    Start at our home page http://xena.ucsc.edu/ and click on 'Launch Xena'. You are now in our Visual Spreadsheet Wizard.
  2. 2.
    Type 'GDC TCGA Lung Adenocarcinoma (LUAD)', select this study from the drop down menu, and click 'Done'.
  3. 3.
    Type 'EGFR', select the checkboxes for Gene Expression, Copy Number, and Somatic Mutation, and click 'Done'.

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).
Making your own Visual Spreadsheet: Which TCGA study to choose

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. 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. 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. 3.
    Zoom in on a column. Click and drag within column D. Release to zoom.
  4. 4.
    Zoom out on a column. Click the red zoom out text at the top of column D.
  5. 5.
    Zoom in on samples. Click and drag vertically in any column in the Visual Spreadsheet to zoom in on these samples.
  6. 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

More information

Test your knowledge

Question 1
Answer 1
Create a Visual Spreadsheet looking at TP53 gene expression and mutation in samples from patients in the GDC TCGA Lower Grade Glioma study.
Question 2
Answer 2
Change the Visual Spreadsheet from Question 1 so that the patient's samples are sorted by mutations rather than gene expression.