BGI WEGO Web Gene Ontology Annotation Plotting

sample figure
Fig 1. The sample figure of WEGO output, from the rice genome paper published on science.
The GO (Gene Ontology) project began as the collaboration of Flybase, Saccharomyces Genome Database (SGD) and Mouse Genome Base. And now it has gone beyond what it used to be. There are so many GO resources and tools that help biologists explore the depth of gene analysis, from several genes to large-scale.
WEGO (Web Gene Ontology Annotation Plot) is a useful tool for plotting GO annotation results. It has been widely used in many important biological research projects, such as the rice genome project [Yu, J. et al. Science 296, 79-92 (2002); Yu, J. et al. PLoS Biol 3, e38 (2005)] and the silkworm genome project [Xia, Q. et al. Science 306, 1937-40 (2004)]. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO along with two other tools, namely External to GO Query and GO Archive Query, are freely available for all users. Any suggestions are welcome at Here is a sample output generated by WEGO (Fig. 1).
There are three steps to work with WEGO. The first is to upload annotation result(s). The input file(s) can be in WEGO native format, or if you are using InterProScan as the annotation tool, the result(s) could be used directly. We support InterProScan text, raw and XML output formats as the input format of WEGO. Then, you will be redirected to a webpage with hierarchical GO tree in which all the GO terms contained in the files uploaded are included. You could choose any GO terms interested at this page to display in the output histogram. The last step is figure setting, such as the figure caption, histogram color(s) and legend description. Currently, WEGO support SVG, PNG, PostScript, EPS and GIF as output graph format. You can also get the results by our feedback Email.

Cite WEGO:
  Ye J, Fang L, et al. Nucleic. Acids Res., 2006, 34(Web service issue), 293-297  [PDF]

Begin WEGO [ sample of input files ]   [ launch WEGO demo ]
GO archive:   Input file format:
Input file 1:
Input file 2:
Input file 3:

Previous analysis ID: Refresh GO archive:
[WEGO Resources]
External to GO Query
GO Archive Query

[WEGO mirrors]
Backup site
Hangzhou mirror
SWU mirror

[GO Documents]
Gene ontology documents
GO flat file format guide
OBO flat file format guide
XML version guide
MySQL version guide

[GO Resources]
The Gene Ontology homepage
The Sequence Ontology
Saccharomyces Genome Database
Mouse Genome Informatics
The InterProScan homepage
The GOA homepage
Cluster of Orthology Groups

[GO Tools]
GO Term Finder

[SVG Tools]
Inkscape SVG Editor
Adobe SVG viewer
Apache SVG Tools

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