Galaxy

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Revision as of 01:48, 5 April 2013 by Cjm (talk | contribs)
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Current URL: http://galaxy.berkeleybop.org

The GO website lists >50 tools for doing GO-based analyses but these are not well integrated. AmiGO/GOOSE offers some functionality such as slimming, enrichment, data extraction but these are difficult to chain together. A simple integrated environment in which tools could be linked in workflows would be beneficial to the community.

The GO Galaxy instance is an environment to do all your analyses in one place

  • term enrichment
  • format conversion (e.g. obo to owl)
  • annotation file munging (e.g. mapping to slim)

Using GO Galaxy

Basic Term Enrichment

  1. First upload your gene set. Select "Get data > upload file".
  2. OPTIONAL: upload a population gene set (required for Ontologizer)
  3. Bring in the latest version of GO into your instance. Select "OBO/OWL Tools" and "fetch ontology". Type "GO" in the box.
    1. TIP: when the ontology come in click on "attributes" (the pen symbol) and rename this "GO"
  4. Bring in the latest version of GO into your instance. Select "Annotation > Fetch associations"
  5. Select "Term enrichment / GO termfinder"
    1. Enter the number of background genes in the genome, or an estimate
    2. Make sure your uploaded genes go into the "genes" selection
    3. Make sure GO and your GAF go into the respective fields
    4. Execute

the results here is a human-readable report file

Term Enrichment using Ontologizer

Follow the steps above, with the additional steps or modification

  1. Upload a population gene set.
    1. If you wish to consider all annotated genes, use "Text manipulation / cut" to select col3 from your GAF
  2. Select "Term enrichment / ontologizer"
    1. There are a variety of methods - consult the ontologizer site for details. try Parent-Child and Bonferoni as default
    2. Execute

Note that this produces two outputs - a tabular file that can be processed further and a visual display with enriched terms highlighted




Source

We maintain the GO/OBO galaxy tool configurations and helper scripts as a fork off of the main galaxy-dist repo in bitbucket.

Installing locally

1. install mercurial
2. Type:
  hg clone https://bitbucket.org/cmungall/galaxy-obo
3. Follow the instructions in README-galaxy-obo.txt
  more README-galaxy-obo.txt

Term Enrichment Format

See Is there a standard format for TE results?

  • TERF project on googlecode

Publications

Erick Antezana, Aravind Venkatesan, C J Mungall, Vladimir Mironov, Martin Kuiper (2010) ONTO-ToolKit: enabling bio-ontology engineering via Galaxy, BMC Bioinformatics 11 (Suppl 12)