GO Module

Page Sections

 

Viewing Assigned Terms

When we imported the InterPro analysis results, the InterPro terms were assigned to the mRNA features. We also requested when we created the InterPro Analysis page that it parse GO terms from the results. As a result, GO terms have also been assigned. Also, when importing the KEGG results, KEGG orthologs and pathways were assigned to features. Therefore, we now have a new Annotated Terms item in the table of contents. For our example feature (http://localhost/feature/citrus/sinensis/mRNA/PAC%3A18136219), the results are as follows:

Tripal2.0 feature terms.png

Because we now have GO terms associated with features we can setup the GO report that appears on the organism page. Navigate to the Citrus sinensis organism page and click the Go Analysis Reports in the Resources sidebar. A page appears with instructions to the site administrator that gives details to make the report visible.

Follow the instructions as presented on the page. Briefly, you need to

  1. Set the CV term paths for the three GO vocabularies. This should have been done automatically when you loaded the Gene Ontology earlier in the Tutorial.
  2. Populate the go_count_analysis materialized view.

When complete the following report will be visible:

The GO report provides pie charts and an expandable tree for browsing results. Clicking on a GO term in the true will cause a box to appear with details about the term and a link to download a FASTA file of all features annotated with the term. Notice that the graphs are quite simple and the graph for the cellular component is missing. This is because we only loaded GO assignments for a single gene.

The GO Module will also add a new link to the Resources sidebar of any features that have GO terms associated.  The following screen shots shows the GO table added to the orange1.1g015632m mRNA page: