Analysis Menu

This menu contains various data-analysis features. These functions will be discussed in detail in the following sections.

  1. GO-Slim
  2. Enzyme Code and KEGG
  3. Coding Potential
    1. Rfam
    2. Coding Potential Assessment (See Blast2GO App section, Coding Potential)
  4. Enrichment Analysis (Fisher's Exact Test)
  5. Gene Set Enrichment Analysis (GSEA)
  6. Find Orthologs Groups (COG) (See Blast2GO App section, Orthologous Groups)

Image b2g_analysis_menu

Figure 1: Analysis Menu Options


GO-Slim

GO-Slim is a reduced version of the Gene Ontology that contains a selected number of relevant nodes. The Run GO-Slim (online) function (under the Analysis → GO-Slim menu) generates a GO-Slim mapping for the available annotations. Different GO-Slims are available which are adapted to specific organisms. Blast2GO supports the following GO-Slim mappings: General, Plant, Yeast, GOA (GO-Association) and TAIR.

Use the Analysis > GO-Slim > Remove GO-Slim option to return to the original annotations.

Enzyme Code and KEGG

Blast2GO provides EC annotation through the direct GO > EC mapping file available at the GO website. This means that only sequences with GO annotations will eventually show also EC numbers and that the GO annotation accuracy can be made extensive to Enzyme annotations.

Additionally, the KEGG map module allows the display of enzymatic functions in the context of the metabolic pathways in which they participate. Select the sequences of your interest and go to Analysis > Enzyme Code and KEGG > Load Pathway-Maps from KEGG (online). The application will search all KEGG maps containing the EC numbers of the selected sequences and make them available at the KEGG Maps tab. The list of found KEGG maps will appear at a new results tab. By clicking on a given pathway, it will be loaded on the left graphical window. Sequences and EC codes contained in that pathway are shown in the lower frame, and highlighted with different colors (one color for each EC) in the pathway map.

It is possible to load the KEGG pathway map of only one sequence on the context menu (see image below). It will show the KEGG maps associated to that particular sequence.


Image loadkegg

Figure 2: Load Kegg Pathway Map


Statistics

To see the main Enzyme classes in the dataset it is possible to generate a distribution Enzyme Code chart on "charts" icon.

  • Main Enzyme Classes: Shows the distribution of the 6 main enzyme classes over all sequences.
  • Second Level Classes: Same as above but for the corresponding subclass.


Image enzymedist

Figure 3: Enzyme Code Distribution

Image enzymecode

Figure 4: Enzyme Code Statistic