What is Gene set enrichment?

Enrichment analysis is a technique commonly used to add biological context to a list of genes, such as list of significant genes filtered from differential analysis report. The procedure is based on assigning genes to groups and then finding overrepresented groups in filtered gene lists using a Fisher's exact test.

Running Gene set enrichment

We recommend filtering to a set of genes you want to test for enrichment, but Gene set enrichment will run on any Feature list data node. 

• Click a Feature list data node
• Click the Biological interpretation section of the toolbox
• Click Gene set enrichment 
• Configure the background gene list (optional)

The background gene list is used as the list of possible genes. By default, this is the genes included in the selected gene set database. If your assay limits the genes that could be detected, you may want to specify a background list.

• Choose the Gene set 

The gene sets available for the current Assembly are listed under the Gene set drop-down list. The assembly is automatically selected, if possible. If the assembly cannot be detected, you can specify it using a drop-down menu.

• Click Finish to run (Figure 1)

Figure 1. Selecting the gene set for Enrichment analysis. Sets available for the current Assembly are listed under Gene set

By default, the groups are defined by Gene Ontology (GO), a bioinformatics initiative to unify the representation of gene and gene product attributes across various species [1, 2].

Alternatively, selecting the Add gene ontology source from the Gene set drop down list option opens another dialog (Figure 3), where you can either Download gene set from Partek^® (Recent GO database gene sets for human, mouse and rat are available) or Import gene set. The latter option takes you to the file browser, where you can point to the file that you want to use (not shown). Partek^® Flow^® accepts .gmt files as gene set inputs.

Figure 2. Adding gene set files via Create gene list dialog. Download gene set obtains a gene set file from Partek (human, mouse and rat are supported), Import gene set opens a file browser, which is used to specify the file that should be added to the Library file management functionality

The result is stored under an Enrichment task node. To open it, double click on the node or select the respective Task report from the context sensitive menu.

Gene set enrichment task report

Figure 4 shows an example Gene set enrichment task report. The table contains one gene set per row (Gene set column; the column entries are hyperlinks when using the distributed GO gene sets), with the category name in the Description column. The categories are ranked by the Enrichment score, which is the negative natural logarithm of the enrichment p-value (P-value column) derived from Fisher's exact test on the underlying contingency table. The higher the enrichment score, the more overrepresented the GO category is within the input list of significant genes. The columns can be searched by typing in the search term in the respective box (and hitting Enter), or sorted by selecting the double arrow icon ( ).

Figure 3. Go enrichment report (truncated). Gene set column contains Gene Ontology identifiers (hyperlinks). Category labels are in the Description column. Enrichment score: negative natural logarithm of the enrichment P-value derived from the Fisher's exact test. Genes in list: number of genes that are present both in the list of significant genes and the gene set (GO category). Genes not in list: number of genes that are present in the gene set, but are not present in the list of significant genes. The column on the right contains links to gene breakdown chart and extra details

The contingency table (Figure 5) can be displayed by selecting the View gene breakdown chart icon on the right (). The term "list" refers to the list of significant genes, while the term "set" refers to the respective GO category. The first row of the contingency table is also seen in the report, namely the Genes in list and Genes not in list columns.

Figure 4. Contingency table used to calculate the enrichment p-value. List refers to the list of significant genes, set refers to the gene ontology category

The View extra details () button provides additional information on the GO category (Figure 6). In addition to the details already given in the report, a full list of Genes in list and Genes not in list can be inspected and downloaded (Download data) to the local computer as a text file.

Figure 5. Gene ontology enrichment extra details

As previously mentioned, if you are using the GO gene sets distributed by Partek, the GO identifiers in the first column are hyperlinks to the Gene Ontology web-site entries (an example shown in Figure 7).

Figure 6. Selecting a GO category in the table report opens up a browser and displays additional information on that category via GO web-page

Visualizing gene set enrichment results

If the gene set enrichment table has fewer than 100 results (rows), the GO categories can be visualized in the Data Viewer. Otherwise, a notification is displayed in the top left corner (Figure 7).

If needed, filter down the number results, for instance by using a cut-off based on the enrichment score. Type in the cut-off value in the text box beneath the Enrichment score and hit enter (an example is shown in Figure 8). Once the number or results falls below 100, a link to the Data Viewer will be displayed (Figure 8). Click on the View plots in Data Viewer link to open a new Data Viewer session. 

Two plots are loaded into Data Viewer (Figure 9). Both plots show enrichment score on the horizontal axis and gene ontology categories (i.e. the ones present in the gene enrichment table) on the vertical axis. The plots show enrichments scores (Enrichment score column of the gene ontology table) and - in addition - the plot on the left uses color range to depict enrichment P-value (green = low, red = high P-value). 

The same functionality is available for pathway enrichment results. 

References

1. Ashburner M, Ball CA, Blake JA et al. Gene Ontology: tool for the unification of biology. Nat Genetics. 2000; 25:25-29.
2. The Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucleic Acids Res. 2015; 43:D1049-1056.Recommended citations from the Geneontology.org website

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