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| SubtitleText | Configure the parameters of the GO enrichment test |
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| AnchorName | Cinfigure_GO_test |
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At this point, I get a dialog asking me to specify the probeset annotation. |
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 (
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| SubtitleText | For an explanation of the different kinds of mapping file supported, click the help icon next to each one |
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| AnchorName | select_mapping_file |
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A new spreadsheet (Figure 4) and the gene ontology browser (Figure 5) will appear.
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At this point, I get  Image Added
Select, yes to get  Image Added
Checking the genomic properties of Gene_List.txt, I see  Image Added
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? |
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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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