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Advanced Tutorial: Section 2
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 made for those who have basic knowledge 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.
Part A: 10 min
Part B: 5 min
Part C: 15 min
- 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.
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.
- 2.Type 'TCGA Breast Cancer (BRCA)', select this study from the drop down menu, and click 'To first variable'.
- 3.Choose 'Phenotypic', select 'sample_type' from the dropdown menu, and click 'To second variable'.
- 4.Choose 'Phenotypic', click on 'advanced', type 'pam' into the search bar, select 'PAM50Call_RNAseq' from the dropdown menu, and click 'Done'. This will exit the wizard.
- 5.Click on 'Click to insert a column' after column C. Copy and paste the 50 genes, choose 'Gene Expression', and click 'Done'.
- 6.Click the handle in the lower right corner of column D, mutation. Move it to the right to make the column bigger.
List of 50 genes used to calculate the PAM50 subtype call:
UBE2T BIRC5 NUF2 CDC6 CCNB1 TYMS MYBL2 CEP55 MELK NDC80 RRM2 UBE2C CENPF PTTG1 EXO1 ORC6L ANLN CCNE1 CDC20 MKI67 KIF2C ACTR3B MYC EGFR KRT5 PHGDH CDH3 MIA KRT17 FOXC1 SFRP1 KRT14 ESR1 SLC39A6 BAG1 MAPT PGR CXXC5 MLPH BCL2 MDM2 NAT1 FOXA1 BLVRA MMP11 GPR160 FGFR4 GRB7 TMEM45B ERBB2
- 1.Click on the picker icon next to the filter menu to enter pick samples mode.
- 2.Click on the Primary Tumor samples.
- 3.Click the filter menu and select 'Keep samples'.
- 4.Exit pick samples mode by clicking on the picker icon again.
- 5.Click the filter menu and select 'Remove samples with nulls'.