The setup dialog for GO ANOVA can be found in the Biological Interpretation section of the expression workflows (Gene Expression, MicroRNA Expression, Exon, RNA-Seq, miRNA-Seq). It is recommended that GO ANOVA is run on the sheet with expression levels, after import and normalization, though GO ANOVA can be run on any spreadsheet with samples on rows and genes on columns. If a child spreadsheet is selected, such as the result of a prior ANOVA analysis, then the test will be automatically run on the parent spreadsheet.

Upon selecting GO ANOVA (Biological Interpretation > Gene Set Analysis), Partek Genomics Suite will first offer the opportunity to configure the parameters of the test and exclude functional groups with too few or too many genes (Figure 1). To save time when running GO ANOVA, the size of GO categories analyzed can be limited using the Restrict analysis to function groups with fewer than __ genes. Large GO categories may be less interesting and also take the most time to analyze. We recommend to restrict the analysis to the groups with fewer than 150 genes, as it can make the analysis much quicker (and the results easier to interpret). In the current example, the maximum category was set to only 20 genes, for demonstration purposes only.

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