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One of the main functions of GO enrichment is to find the overrepresentation of functional categories in a gene list. With the Gene_List.txt spreadsheet selected:

• From the Gene Expression workflow, choose Biological Interpretation followed by Gene Set Analysis
• Select the GO Enrichment radio button in the Gene Set Analysis dialog (Figure 1) followed by Next
• In the next dialog, make sure the Gene_List.txt spreadsheet is chosen from the dropdown drop-down list and click Next

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SubtitleText Gene set analysis dialog. Choose GO Enrichment and select Next AnchorName Gene Set Analysis dialog

You have the choice to use the Fisher's Exact or Chi-Square test. Both tests compare the proportion of a gene list in a functional group to the proportion of genes in the background for that group. Both are acceptable and you can always test both by re-running the analysis. You can also restrict the analysis to functional groups with more than or fewer than a specified number of genes. Restricting the analysis to GO groups with fewer than 150-200 genes will increase the speed of analysis and exclude large groups which may not be too informative. If analysis time is not a concern, you can just use the default settings.

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SubtitleText GO enrichment output spreadsheet. Right-click a row header to perform additional tasks on a chosen GO term AnchorName GO enrichment output

The new spreadsheet (GO-Enrichement.txt) is a child spreadsheet of the gene list. The first column contains the GO functional groups, each of which falls into a broader category (biological process, cellular component or molecular processes), shown in column 2. The GO functional groups are sorted by descending enrichment score, which is shown in the third column 3. The enrichment score is the negative natural logarithm of the enrichment p-value, which is shown in column 4. The higher the enrichment score, the more over-represented overrepresented a functional group is in the gene list. If a functional group has an enrichment score of over 1, it is over representedoverrepresented. As a rule of thumb, an enrichment score of 3 corresponds to significant over representation overrepresentation (p-value=0.05). For your data, you may wish to add a multiple test correction (e.g. FDR) by going to Stat > Multiple Test correction. We will not perform the multiple test correction for this tutorial.

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• On the GO-Enrichment.txt spreadsheet, right-click on a row header of a functional group, such as hydrogen ion transmembrane transporter activity, which has an enrichment score of 29.9484, and choose Browse to GO term from the menu
  

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A new spreadsheet (gene-list) will be created (Figure 6) which  that contains the genes in the original list that belong to the chosen functional group will be created (Figure 6). Note that this spreadsheet is a Partek temporary (ptmp) file. To save it, click the Save icon (Image RemovedImage Added).

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SubtitleText New gene list spreadsheet containing all the genes in the original list that belong to the chosen functional group AnchorName gene list

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