How do I compare gene expression between subgroups?

  1. First, make sure that the gene or genes that you want to compare across your groups are on screen.

  2. Click on the charts icon in the top right and choose 'Compare subgroups'.

  3. Click the dropdown for 'Show data from' and choose your gene expression column.

  4. Click the dropdown for 'Subgroup samples by' and choose your subgroup column.

  5. Choose if you would like a box plot or violin plot and click 'Done'.

Example

Below we look at patient's samples that have aberrations in EGFR in the TCGA Lung Adenocarcinoma study. We will investigate if patient's samples that have aberrations in EGFR (mutations or copy number amplifications) have higher expression.

https://xenabrowser.net/?bookmark=d31da9334a490d3cc5b5b75446e679a1

Steps

  1. Click the graph icon in the upper right corner to enter Chart View.

  2. Click 'Compare subgroups', since we want to compare the group of samples who have aberrations in EGFR to the group of samples that do not.

  3. Click the dropdown for 'Show data from' and choose 'column C: EGFR - gene expression RNAseq - HTSeq - FPKM-UQ'.

  4. Click the dropdown for 'Subgroup samples by' and choose 'column B: (mis OR infra) OR C:>0.5 - Subgroup'.

  5. Click 'Done'.

Video of steps

For more information see our Basic Tutorial: Section 3.

Last updated

Was this helpful?