How to combine pairwise differential expression results with a functional annotation project in OmicsBox?

How to combine pairwise differential expression results with a functional annotation project in OmicsBox?

Once differential expression results are retrieved, it could be interesting to assign functional annotations to the differentially expressed genes and visualize the results in a single project. This is possible in OmicsBox.

Our starting point will be the transcriptomic sequences we used in the differential expression analysis. These sequences must be annotated (Functional Analysis > Blast, Blast2GO Mapping, and Blast2GO Annotation) and saved in an OmicsBox project.

From here, it is possible to combine the differential expression results and the annotation via File Manager (View > File Manager). To combine the projects:

  1. Select both projects.
  2. Right-click on one of them and select “Open Pairwise Results“.

Figure 1: Combining Differential Expression Results and Functional Annotations via File Manager.

A new table should open now in OmicsBox, with the combined information of both projects. In this table, it is possible to explore the functional annotations of the up-regulated or the down-regulated genes using the Filters.

Figure 2: Table with Differential Expression and Functional Annotation data combined.

For example, imagine that we are interested in knowing the functional annotations of the down-regulated genes. We can use the filters in the Tag column: “DOWN” and “ANNOTATED”.

Figure 3: Filtering down-regulated and annotated genes.

This tutorial provides an easy way to check the functional annotations of the sequences individually. To achieve further biological insight one can launch an Enrichment Analysis (Fisher’s Exact Test or GSEA) from this table. On the toolbar, click on the “Fi” icon to perform a Fisher’s Exact Test, or on the “Ge” icon to perform a GSEA providing the original annotations as Reference Set. Please note that the annotation project should be exported first to a “.annot” file if running a Fisher’s Exact Test.
For further information on how to launch an enrichment analysis from pairwise differential expression results, please link here.
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