Basic Tutorial: Section 3

Covers Chart View and adding new columns of data to a view

Description

This tutorial is intended for those who have never used Xena before but who have completed Section 1 of the Basic Tutorial (completion of Section 2 is recommended but not required). We will cover how to make box plots and bar charts using our Charts and Statistics View and how to add another column of data, in particular phenotype data, to the view.

Prerequisites

This tutorial assumes completion of the Basic Tutorial: Section 1. Completion of Basic Tutorial: Section 2 is recommended but not required. This tutorial begins where the Basic Tutorial: Section 2 ends. A live link to the end of Basic Tutorial: Section 2 is provided at the beginning of this tutorial.

Estimated time needed

Part A: 5 min

Part B: 15 min

Learning goals

Part A

  • Create a box plot using the Charts and Statistics View

Part B

  • Add another column of data to the view

  • Add phenotype data to the view

  • Create a bar chart using the Charts and Statistics View

Tutorial

In the Basic Tutorial: Section 1 we found that we found that samples that have aberrations in EGFR (mutations or amplifications) have higher expression.

In the Basic Tutorial: Section 2 we created two subgroups: those with aberrations and those without aberrations in EGFR. We ran a Kaplan Meier survival analysis and found that there was no survival difference between these two groups.

Now we are going to use the subgroups created in the Basic Tutorial: Section 2 to see if there is a statistical difference in expression between the two subgroups and whether males or females have more aberrations.

To ensure your columns are sorted the same as those in this tutorial, please start at this link: https://xenabrowser.net/?bookmark=2862e84d66d5c2e1a99a44fd4e2c4045

Part A

We found that samples that have aberrations in EGFR (mutations or amplifications) have higher expression. Now we are going to investigate if this difference in expression statistically significant.

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

Part B

We will now investigate how EGFR aberrations compare between men and women.

https://xenabrowser.net/?bookmark=ab3dc8bc827a2aaa9ae75d8c82629a3d

Steps

  1. Click the 'x' in the upper right corner to exit Chart View.

  2. Hover between columns B and C until 'Click to insert a column' becomes visible. Click on it.

  3. Choose 'Phenotypic'

  4. Type 'gender' into the search bar.

  5. Select 'gender.demographic' from the dropdown menu.

  6. Click 'Done'.

  7. Click the column menu at the top of column C and choose 'Chart & Statistics'. Note that this is just another way to enter Chart View.

  8. 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.

  9. 'column C: gender.demographic' should already be selected for 'Show data from'. If not, select it.

  10. 'column B: (mis OR infra) OR C:>0.5 - Subgroup' should already be selected for 'Subgroup samples by'. If not, select it.

  11. Click 'Done'.

Video of steps 1-6

Video of steps 7-11

Test your knowledge

Question 1
Answer 1
Question 1

Starting at the end of Part A, create a violin plot that compares copy number variation between samples that have EGFR aberrations and those that do not.

Question 2
Answer 2
Question 2

Starting at the end of Part B, add the phenotype data 'age_at_initial_pathologic_diagnosis' to the plot.

Answer 2

Ending Screenshot

Note that your column order may be different.

https://xenabrowser.net/?bookmark=e3a364e74e74a9dbeb7f23b8c286456e