How to identify pathways, diseases, or phenotypes that are enriched in a gene set?

Find potential underlying association in a gene set with the built-in Analytics set enrichment analysis. For example, what are the top most associated pathways, diseases, or phenotypes with a particular gene set?

pathway_enrichment

Steps

Note:

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A visible item on the platform, such as a [link] or a [button], is in square brackets.

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1. Create or open an Analytic project. Enrichment analysis works best for gene sets.

2. Select the genes of interest in the [Data Selection] section.

3. Scroll down to the [Method Selection] section.

gene_set_enrichment_selection4. Click on the [Find Related] tab to access the categories for the enrichment analysis. 

Note: More categories and sub-categories can be found by clicking the [Select a Category] button. Refer to this article for more details on these sub-categories for gene set enrichment.

5. Click a category button to do an enrichment analysis. A table appears showing the results sorted by Fisher's exact test p values from smallest to largest. Refer to this article for more detailed description on how to interpret results from an enrichment analysis.

  • Click [Pathway Analysis] to find associated pathways
  • Click [Disorder Analysis] to find associated diseases
  • Click [Phenotype Analysis] to fine associated phenotypes

6. To drill down on the results, click the number of associated concepts to review the list of genes. 

pathway_analysis_results7. A pop-up window appears showing the classification and localization of each gene as well as the number of references that exist for each gene and the selected concept (e.g. apoptosis):

drill_down_pathway_analysis

  • Click the [save icon] to save the list of genes.
  • Click the [Publications] column header to sort the genes based on the number of references.
  • In the [Publications] column, click on the number of publications to review all the references. A pop-up window opens showing 10 publications per page. 
    • Click the [Open full search page] link located near the top of the pop-up window to get all the search results. This brings you to Search where you can access  all the search results and filter the search results.
      publication_pathway_enrichment
    • Click on the title of the publication to open the publication detail page. 

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