This tutorial is intended for those who have never used Xena before. We will cover how to create your first Visual Spreadsheet with gene expression, mutation, and copy number variation data.
This tutorial assumes a basic understanding of
cancer processes that can lead to altered gene expression, such as copy number variation or mutations
RNAseq gene expression, copy number variation, and mutational genomic sequencing data
The Cancer Genome Atlas (TCGA)
These resources can help you gain a basic understanding of these concepts:
Part A: 5 min
Part B: 10 min
Create a Visual Spreadsheet
Compare data across columns
Zoom in and out
We are going to be examining EGFR aberrations in patients with lung adenocarcinomas using TCGA data. We will be looking at mutation and copy number aberrations and how they affect gene expression.
Our goal is to build a Visual Spreadsheet and understand the relationship between the columns of data.
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 'Done'.
Type 'EGFR', select the checkboxes for Gene Expression, Copy Number, and Somatic Mutation, and click 'Done'.
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.
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)
To further explore the relationship between the gene expression, mutation, and copy number variation data for EGFR, we will move columns to change the sort order, resize columns, and zoom in both for the entire Visual Spreadsheet and within a column.
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.
Create a Visual Spreadsheet looking at TP53 gene expression and mutation in samples from patients in the GDC TCGA Lower Grade Glioma study.
Change the Visual Spreadsheet from Question 1 so that the patient's samples are sorted by mutations rather than gene expression.