This plugin is designed for fast generating user data given that a reference user data is loaded. All we need to do is to (1) select a reference from user tree, (2) assign a name for the new data, and (3) give an accession list of the new data. Specifically, you would have found this plugin useful if you are going to do GO-enrichment analysis with a reference user data of a whole genome.
In this example, with a reference user data of Arabidopsis thaliana, we present how to do GO-enrichment analysis using this plugin and the MultiView plugin step by step.
File -> Load, open the file "Arabidobsis.reference.tree". A user tree node named "reference" will be loaded, which contains 27235 locus accessions of arabidobsis protein-coding genes.
Plugins -> FastInput, a wizard of this plugin will be showed.
In this example, we are going to extract user data of transcription factors from the reference, so select "reference" as the reference and input "TFs" as the name of the new tree node. Then click the "Next" button. Note that the "Next" button will be disabled if you input a name that is the same with some existing node.
The next window asks for gene accessions of TFs. Open the file "At_Transcription_factors.txt" with any text editor. This file contains accessions of TFs, 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.
A minor message window will appear, which tells accessions that are not in the specified reference. In this example, they are not protein-coding genes in the TAIR database. Examine them if you like. Click "OK" to finish this plugin.
A node named "TFs" will be added in the user tree. This node contains 1,815 arabidobsis transcription factors.
Invoke the MultiView plugin and perform a GO-enrichment analysis. You will find that regulation-related GO terms are ranked at the top.
The reference user data of Arabidopsis thaliana, i.e., the file "Arabidobsis.reference.tree", integrates information like locus accessions, gene symbols, descriptions, GO annotations, and AraCyc pathways. You may use this plugin and the Listing plugin to build a table of any gene list that includes any information as you like.