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A new spreadsheet (Figure 4) and the gene ontology browser (Figure 5) will appear.

Comment

At this point, I get

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Select, yes to get

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Checking the genomic properties of Gene_List.txt, I see

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I downloaded the zipped folder by selecting the link in the first section of the tutorial; maybe there's an issue with the annotation file in the folder at that link?

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 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 overrepresented a functional group is in the gene list. If a functional group has an enrichment score of over 1, it is overrepresented. As a rule of thumb, an enrichment score of 3 corresponds to significant 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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The Gene Ontology Browser opens in a separate tab (Figure 5). A functional group viewed in the browser will show the hierarchical relationship to the other GO terms. The selected functional group will be highlighted on the left. In Figure 5, you can see the hydrogen ion transmembrane transporter activity is found in the tree molecular function > transporter activity > substrate-specific transmembrane transporter activity > cation-transporting ATPase activity > inorganic cation transmembrane transporter activity > monovalent inorganic cation transmembrane activity. On the right, a bar chart shows the sub-groups of the selected group and their respective enrichment scores.

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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 ().