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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

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Enrichment

Gene set enrichment task can be invoked on a differential analysis output (or filtered differential analysis output) data node or filtered count matrix data node. Since the data node including all the features will server as serve as background, to get a meaningful result, always use a data node containing subset of features to invoke this task. Only gene names will be used in the computation. 

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• Gene set database is user defined database, see more details in the Adding a Gene Set chapter. The gene sets available for the current Assembly are listed under the Gene set  database drop-down list (Figure 2). The assembly is automatically selected, if possible. If the assembly cannot be detected, you can specify it using a the drop-down menu.
  
  

Partek distribute distributes Gene Ontology (GO) for human and mouse genomes, a bioinformatics initiative to unify the representation of gene and gene product attributes across various species [1, 2].

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• Select feature identifier (optional) can be used to specify the feature format (e.g. Gene name, Gene ID, Feature ID). 
• Specify the background gene list (optional) can be used for a feature list. Select the list using the drop-down. Click here for more information on List management.

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.

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The contingency table (Figure 4) 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.

The View extra details () button provides additional information on the GO category (Figure 5). 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. Use the arrow to expand these sections. 

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 6).

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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 11). 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 12). 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). 

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