User manual, GOTaxExplorer, Version 1.0

Comparing biological processes from fungi and mammals

In order to compare the biological processes of two species groups, it is necessary to find the taxonomy identifier for them. The taxonomic tree can be loaded into the tree pane on the right of the query frame which makes it easy to find the accession numbers for mammals and fungi. A double-click on the tree inserts the respective entity into the query. The full query reads


	GO WHERE TAX:4751 RESTRICT TT:biological_process SIM
	  GO WHERE TAX:40674 RESTRICT TT:biological_process

The first part selects all biological process terms from fungi, set 1, which includes all fungal species in the database, and the second part returns the set with all processes from mammalian species, set 2. The table with the results can be separated into three parts.

**Figure 4:** Result frame showing a table with the results from a GO comparison. The table contains the information on the most similar term from set 2, according to sim_Rels and Lin, for each term from set 1.

First, the rows contain the accession number and the name of the GO term in set 1. The second part gives the most similar term from set 2 according to sim_Rel with similarity, accession number and name. The last part contains the information on the most similar term according to Lin. The visualizations of the graph contain also the similarity values. The 2D tree view includes them in parentheses after the name.

**Figure 5:** The window shows the tree view of the biological process with results from a GO set comparison. Each term in set 1 is compared to each term in set 2. All terms from set 1 and their ancestors are colored red and the highest similarity to any term in set 2 is added to the name of the hits in parentheses. The first number is the similarity according to sim_Rel, the second according to Lin.

This allows to browse the graph without jumping between two windows.