Learn how to use the pick samples feature, how to view multiple genes in a single column, how to view a signature, and how to run a differential expression analysis
This tutorial is intended for those who have a basic understanding of how to use Xena. We will cover how to use the pick samples feature, how to view multiple genes in a single column, how to enter and view a signature, and how to run a differential expression analysis between your subgroups.
Create a visual spreadsheet with single column with multiple genes.
Filter to only Primary Tumor samples using the Pick Samples mode.
Remove nulls using the option in the filter menu
Enter and view a gene expression signature
Run a differential expression analysis.
We will investigate the PAM50 molecular subtypes in breast cancer. PAM50 is a 50-gene signature that classifies breast cancer into five molecular intrinsic subtypes: Luminal A, Luminal B, HER2-enriched, Basal-like, and Normal-like.
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We will make a visual spreadsheet where we can explore the relationship between the PAM50 subtype call and the 50 genes that make up the PAM50 subtype call.
We will now look at the TFAC30 gene signature and see how it relates to the PAM50 subtype calls. This gene expression signature over 30 genes predicts pathologic complete response (pCR) to preoperative weekly paclitaxel and fluorouracil-doxorubicin-cyclophosphamide (T/FAC) chemotherapy.
Click on 'Click to insert a column' after column D. Copy and paste the signature below, choose 'Gene Expression', and click 'Done'. Note you need to include the '=' as this tells Xena that you want the signature rather than to see all the genes individually.