It is possible to directly run Functional Enrichment Analysis either GSEA or Fisher Exact Test from a pairwise differential expression analysis executed in OmicsBox in the Transcriptomics Module.
The list of interesting genes will be generated automatically by OmicsBox and there is no need to create it.
Run Fisher’s Exact Test from DiffExp (.b2g/.box) project:
On the toolbar, there is the option to run the Enrichment Analysis.
- Click the Fi icon to run the analysis.
- Select the test set, Up- or Down-regulated genes.
- Provide a .annot file which will be the reference set.
Run GSEA from DiffExp (.b2g/.box) project:
In this case, Blast2GO expects an ordered ranked list, which will be generated automatically and it will use the logFC values.
On the toolbar, it is possible to see the option to run the Gene Set Enrichment.
- Click the Ge icon to run the analysis.
- Provide an annotated Blast2GOproject which will be the reference set.
- It is possible to filter out those genes with higher FDR.
For additional information, please have a look at the user manual.