Performing biological interpretation
To learn more about the biology underlying gene expression changes, we can use gene ontology (GO) or pathway enrichment analysis. Enrichment analysis identifies over-represented GO terms or pathways in a filtered list of genes.
Enrichment analysis
Click the Filtered feature list data node
Click Biological interpretation in the task menu
Click Gene set enrichment then select Gene set database to perform GO enrichment analysis (Figure 1)
Select the latest gene set from geneontology.org from the Gene set database drop-down menu
A gene set enrichment task node and data node will be added to the pipeline (Figure 2).
Double-click the Gene set enrichment task node to open the task report (Figure 3)
The gene set enrichment task report lists GO terms by ascending p-value with the most significant GO term at the top of the list. Also included are the enrichment score, the number of genes from that GO term in the list, and the number of genes from that GO term that are not in the list.
To view the genes associated with each GO term, select to open the extra details page. To view additional information about a GO term, click the blue gene set ID in the first column to open the linked geneontology.org entry in a new browser tab.
For more information about GO enrichment analysis, please see the user guide.
KEGG enrichment analysis
KEGG enrichment analysis identifies pathways that are over-represented in a gene list data node.
Click the Filtered feature list data node
Click Biological interpretation in the task menu
Click Gene set enrichment then select KEGG database
A Pathway enrichment task node and data node will be added to the pipeline (Figure 4).
Double-click the Pathway enrichment task node to open the task report
The Pathway enrichment task report is similar to the gene set enrichment analysis task report (Figure 5).
To view an interactive KEGG pathway map, click the pathway ID (Gene set column).
Additional Assistance
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