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 from healthy and diseased individuals 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:
Part A: 10 min
Part B: 5 min
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.
Create a box plot using the Charts and Statistics View
We will compare MYC gene expression between patient's samples in TCGA colon adenocarcinoma tumor samples and individuals normal colon tissue in GTEx.
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.
Start at our home page http://xena.ucsc.edu/ and click on 'Launch Xena'. You are now in our Visual Spreadsheet Wizard.
Type 'TCGA TARGET GTEx', select this study from the drop down menu, and click 'Done'.
Type 'MYC', select the checkbox for Gene Expression and click 'Done'.
Choose 'Phenotypic' and select the checkboxes for 'sample type', 'study' and 'Primary site', and click 'Done'.
Type 'colon' in the samples search bar and choose 'Keep samples'.
Our goal is to see if the difference in gene expression, where normal samples tend to have lower MYC expression, is statistically significant.
We can now see that patient's tumor samples, both recurrent, primary, and metastatic, have higher expression compared to normal tissue, both patient's matched normal tissue from TCGA and unmatched individual's normal tissue from GTEx.
Click the column menu for column B (MYC gene expression) and choose 'Charts & Stats'
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
Click the dropdown for 'Subgroup samples by' and choose 'column C: Sample Type'.
Leave the chart type as 'box plot', and click 'Done'.
Compare EGFR gene expression between patient's tumor samples and individual's normal lung tissue.