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SubtitleText | GO enrichment output spreadsheet. Right-click a row header to perform additional tasks on a chosen GO term |
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AnchorName | GO enrichment output |
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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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SubtitleText | Viewing a functional group on the gene ontology browser |
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AnchorName | GO browser hydrogen ion |
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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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SubtitleText | New gene list spreadsheet containing all the genes in the original list that belong to the chosen functional group |
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AnchorName | gene list |
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