Tutorial: Tumor vs Normal

Learn how to compare tumor samples to normal samples using our TCGA TARGET GTEx study

Description

This tutorial is intended for those who have a basic understanding of how to use Xena. We will cover how to view tumor and normal samples side by side and how to compare gene expression for one or more genes between tumor and normal samples.

We will be using both GTEx samples as our normal samples as well as TCGA matched normal samples. More information on GTEx normal samples can be found here:

Prerequisites

This tutorial assumes a basic understanding of how to build and read a Visual Spreadsheet. This can be achieved through completion of the Basic Tutorials, especially the Basic Tutorial: Section 1.

Estimated time needed

Part A: 10 min

Part B: 5 min

Learning goals

Part A

  • Build a visual spreadsheet with the columns primary site, sample type, study, and gene expression for the TCGA TARGET GTEx study.

  • Filter to just colon samples.

Part B

  • Create a box plot using the Charts and Statistics View

Tutorial

We will compare MYC gene expression between TCGA and GTEx normal colon samples and TCGA colon adenocarcinoma tumor samples.

Part A

Our goal is to build a visual spreadsheet with the columns 'primary site', 'sample site', 'study', and gene expression for MYC for the TCGA TARGET GTEx study. We will then filter to just samples in the colon.

Steps

  1. Start at our home page http://xena.ucsc.edu/ and click on 'Launch Xena'. You are now in our Visual Spreadsheet Wizard.

  2. Type 'TCGA TARGET GTEx', select this study from the drop down menu, and click 'Done'.

  3. Type 'MYC', select the checkbox for Gene Expression and click 'Done'.

  4. Choose 'Phenotypic' and select the checkboxes for 'sample type', 'study' and 'Primary site', and click 'Done'.

  5. Type 'colon' in the samples search bar and choose 'Keep samples'.

Video of steps 1-4

Video of step 5

Part B

Our goal is to see if the difference in gene expression, where normal samples tend to have lower MYC expression, is statistically significant.

Steps

  1. Click the column menu for column B (MYC gene expression) and choose 'Charts & Stats'

  2. Click 'Compare subgroups', click the dropdown for 'Show data from' and choose 'column B: MYC - gene expression RNAseq - RSEM norm_count' if it is not already selected

  3. Click the dropdown for 'Subgroup samples by' and choose 'column C: Sample Type'.

  4. Leave the chart type as 'box plot', and click 'Done'.

Video of steps 1-4

Test your knowledge

Question
Answer
Question

Compare EGFR gene expression between tumor and normal lung samples.

Answer