VLAD - VisuaL Annotation Display

VLAD is a tool for visualizing GO annotations. The annotation data are a subset of those available at the GO web site. You specify an annotation data set and a set of genes, and the tool will produce a graphical summary of the annotations.

You can now specify your own universe set. See below.
Download a command-line version of Vlad.

Help
(Some...) 		Feedback
(problems? suggestions? requests?) 		Download
Run name:
  • Provides a title for your output.
    (Timestamps are included automatically.)
Vocabularies: Biological Process
Molecular Function
Cellular Component
  • Selects which GO ontologies to show.
  • At least one required.
Annotation Set:
  • Selects annotation database to use.
  • Required.
Annotation Filters: Exclude IEA annotations.
  • If checked, removes annotations supported only by electronic analysis.
Query Set:
Upload file of symbols/IDs:
  • Specifies query set, i.e., your genes of interest.
  • Enter gene symbols and/or IDs into textarea or upload file.
  • Required.
Universe Set:
Upload file of symbols/IDs:
  • Defines base set of genes to compare against.
  • Leave empty to specify all genes in database (the default).
  • Otherwise, enter gene symbols and/or IDs into text area or upload file.
Scoring: Percentages
P-values
  • Specifies scoring method.
  • Choose "Percentages" to get overview of the query set.
  • Choose "P-values" to compare query set against universe.
Display Settings: Generate graphical display.
Generate tabular display.
Pruning threshold.
Collapsing threshold.
  • Controls which portions of the output are shown and how they are drawn.
  • Lower the pruning threshold to include more nodes.
  • Lower the collapsing threshold to draw more nodes in expanded form.
 
Sponsored by MGI.
Graphical display by GraphViz.