Functional Annotations

BioMaps

BioMaps is useful for identifying which functional terms (GO or MIPS functional terms) are enriched in a gene set. It takes one or more set of genes as input and compares the associated functional terms to a background population (e.g. Arabidopsis genome).
To Begin, click on the Analyze link:

Analyze Link

Select the gene list or gene lists by selecting the checkbox in front of your genes in the main view. In the Analysis pull down menu select BioMaps and then click on the Analyze button.

Select Biomaps

This will take you to a form where you can select the term you want to use in your analysis and also the statistics and the p-value cutoff.

BioMaps Form

When the analysis is complete you will provided links to different ways of looking at the data.

BioMaps Results

The table output lists the GO terms that are over-represented and the genes annotated to this term along with AGI code for the genes and the p-value. If you would like to save the list of genes associated to a go-term in the table, simply select the checkbox near the go term and click on Add to Cart

BioMaps Table

In addition, a graphical output is presented that shows GO terms as nodes in a graph, with the relevant genes attached to them. These genes can be added to the gene cart. Here the graph represents the GO-heirarchy and the nodes of the graph are color coded based on the p-value.

BioMaps Network

The Download link will allow you to save the table on your local computer and open it directly with Excel or any other spreadsheet.

Sungear

Sungear is a visualization tool that allows an interactive exploration of many experiments at a genomic scale. To use Sungear simply choose which gene sets you would like to analyze and select Sungear from the Analysis drop down.

Sungear Select

Sungear is a powerful tool and it might be helpful to read the documentation to best use it.

Using Sungear

Using Sungear