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To compare gene expression for malignant cells between astrocytoma and oligodendroglioma subtypes, malignant cells from each sample can be pooled to simulate bulk RNA-Seq data.
Pool cells
- Click the Filtered counts data node
- Expand the Pre-analysis tools section of the task menu
- Click Pool cells (Figure 1)
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The Glioma data node is equivalent to a bulk RNA-Seq gene counts data node and the same analysis steps can be performed on it including PCA and differential expression analysis.
Explore data with PCA
We can use principal components analysis (PCA) to visualize similarities and differences between samples for a cell type.
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Identify differentially expressed genes
Next, we will perform differential expression analysis.
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You will be returned to the Analyses tab and a new Differential analysis filter task will be added. This will produce a new Filtered feature list data node.
Analyze differentially expressed genes
The Filtered Feature list data node is a good starting point for drawing a hierarchical clustering heatmap and analyzing gene set or pathway enrichment.
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