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ReferenceBuild

Contents

  1. Description
  2. An example of creating Arabidopsis reference
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Description

This plugin is designed for entering customized gened-GO annotations via the graphical user interface. Specifically, users may generate a reference annotation GO annotation data of the whole genome, create interested subsets, and performed GO-enrichment analysis.

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An example of creating Arabidopsis reference

In this example, we present how to build a reference user data of Arabidopsis thaliana. With a reference user data, users may enter subsets using the FastInput plugin and perform GO-enrichment analysis using the MultiView plugin.
  1. Plugins -> ReferenceBuild, a wizard of this plugin will be showed.
  2. For doing GO-enrichment analysis, the newly created subtree of reference annotations should be named "reference"

  3. The next window asks for gene-GO annotation entries. Open the file "Arabidobsis.araport11.txt" with any text editor. This file contains gene IDs and their GO annotations, copy all of them (in Windows systems, use <ctrl>-C). Then paste them to the window (in Windows systems, use <ctrl>-V). Then click the "Finish" button.

  4. A node named "reference" will be added in the user tree. This node contains all genes and their GO annotations downloaded from the database.

  5. With this reference user data, users may enter subsets using the FastInput plugin and perform GO-enrichment analysis using the MultiView plugin.