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.

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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.
Evidence Codes
to Exclude
:
IC IDA IEA
IGI IMP IPI
ISS NAS ND
RCA TAS  
  • Annotations with specified evidence codes are remove before processing.
  • "NOT" annotations (e.g., Gene Abc does NOT have function f) are always removed.
  • IC=Inferred by curator; IDA=Inferred from direct assay; IEA=Inferred from electronic annotation; IGI=Inferred from genetic interaction; IMP=Inferred from mutant phenotype; IPI=Inferred from physical interaction; ISS=Inferred from sequence or structural similarity; NAS=Non-traceable author statement; ND=No biological data available; RCA=Reviewed computational analysis; TAS=Traceable author statement
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:
P-values   Percentages
  • 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.
Region(s) of interest:
(Enter one or more GO ids.)
  • Controls which portions of the output are shown and how they are drawn.
  • Lower the pruning threshold to include more nodes. (0 = nothing pruned)
  • Lower the collapsing threshold to draw more nodes in expanded form. (0 = everything expanded)
  • Region of interest (optional). One or more GO ids. If specified, only shows those nodes that are not pruned by score AND are descendants of ROI nodes.
 

Sponsored by MGI.
Graphical display by GraphViz.