Enrichment analysis is a technique commonly used to interpret a list of genes (such as list of significant genes). The procedure is based on assigning genes to groups, based on their characteristics and finding overrepresented groups in filtered gene lists.
Upon selecting a Feature list data node, the Biological interpretation section will become visible in the toolbox. To perform the analysis, select the Enrichment analysis option (Figure 1).

Figure 1. Biological interpretation section of the toolbox, with the Enrichment analysis option

Then select the gene set you want to use (Figure 2). The files available for the current Genome build are listed under the Gene set drop-down list. Click the Finish button to start the analysis.

Figure 2. Selecting the Gene Ontology gene set for Enrichment analysis. Sets available for the current Genome build 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]. There are three main GO groups which are further divided into subgroups:

• biological process
• molecular function
• cellular component

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 (human, mouse and rat are supported) 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 3. 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 toolbox.

Figure 4 shows an example GO enrichment report. The table contains one GO category per row (Gene set column; the column entries are hyperlinks), 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 4. 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 5. 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 6. Gene ontology enrichment extra details

As previously mentioned, GO identifiers in the first column are hyperlinks to the Gene Ontology web-site entries (an example shown in Figure 7).

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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