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 drop-down list and click Next
- Select the Use Fisher's Exact test radio button (Figure 2)
- Make sure the Invoke gene ontology browser on the result check box is selected
- Leave all other settings as default and click Next
Partek Genomics Suite supports different types of mapping files (Figure 3). These are library files that define how genes are organized into functional groups. For an explanation of each type of mapping file, click on the help icon (
) next to each one.- Select the Default mapping file radio button and click Next
There is more information present in the spreadsheet which helps describe the enrichment score, including the percentage of genes in the group that is present in the gene list, the number of genes present in the group that are present in the list and the total number of genes in the group. Because the original gene list was derived from statistical analysis, extra columns will appear for all p-values in the ANOVA model. For example, the Young/Old score and Gender score columns contain the negative natural logarithm of the geometric mean of p-values for each marker/gene present in the list and in the group. These scores represent the level of differential expression of the genes in the functional group. The larger the score, the more differentially expressed the genes are in the group. A score of 3 or greater corresponds to an average p-value of 0.05 or less. For example, the Young/Old score explains how differentially expressed the genes present in the list and in a given group are between the "Young" and "Old" categories.
- 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
- On the GO-Enrichment.txt spreadsheet, right-click on a row header of a functional group and choose Term Details from the menu
A web browser will be opened and you will be re-directed to the AmiGO website, where you will find more details about the chosen GO term (internet connection required).
- On the GO-Enrichment.txt spreadsheet, right-click on a row header of a functional group and choose Create Gene List from the menu
A new spreadsheet (gene-list) 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 (
Additional Assistance
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