Gene Ontology Newsletter
Issue No. 9
May 2008
New AmiGO Release
April 2008 saw a new release of AmiGO, the official GO consortium tool for searching and browsing the GO database. AmiGO 1.5 has a new search engine and incorporates two new tools, Term Enrichment and GO Slimmer. There are also more download options (gene association, RDF-XML, and OBO formats), bar charts to show the distribution of annotations beneath a term, and a slew of improvements and bug fixes, both to the interface and behind the scenes.
AmiGO: A more relevant search
When you search for a gene product or term, AmiGO will now return the results sorted by relevance, bringing more salient hits to the top of the result set. The sort order is customizable, and users can set their sort parameter of choice. If there are no matches in the fields initially specified, AmiGO will automatically search other fields.
Screenshot of the results of searching GO terms for 'transcription'
Enrich Your AmiGO Experience
The Term Enrichment tool can be used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms. The algorithm employed by the tool attempts to determine whether an observed level of annotation for a group of genes is significant within the context of annotation for all genes within the genome; examples of studies that have used this algorithm are PMID:15492223 and PMID:14561723. AmiGO's Term Enrichment tool, which is based on the GO-TermFinder perl module by Gavin Sherlock and Shuai Weng at Stanford University, allows users to specify a list of genes, define a background set against which the significance will be calculated and set the p-value [significance indicator] cut-off. Term enrichment is a very useful method for analyzing data from large scale experiments, such as gene clusters from microarray expression data.
Use the Term Enrichment tool with your data set.
Slim Your GO
Sometimes it can be useful to get an overview of a data set by viewing the high level terms to which gene products are annotated; this is the function of GO Slimmer. GO Slimmer is an adaptation of the map2slim script by Chris Mungall. By mapping the granular annotations of a query set up to a chosen group of broad, high-level parent terms, one can view the distribution of annotations more easily. The GO Slimmer tool simply bins annotations up to high level terms without calculating significance.
Future Plans for Ontology Development
Having successfully implemented the regulates relationships in the biological process (BP) ontology, we now plan to add regulates relationships within the molecular function (MF) ontology and between the BP and MF ontologies. Adding these relationships greatly improves the ability of the ontology to represent biology completely and accurately. This allows users to ask more complex questions, such as "which gene products either regulate kinase activity or are kinases?".
We will make the implied relationships between MF terms and the corresponding 'regulation of molecular function' BP terms explicit. For example:
regulation of kinase activity (BP) regulates kinase activity (MF)
Similarly, we will make implicit regulatory relationships between terms within the MF ontology explicit. For example:
kinase regulator activity (MF) regulates kinase activity (MF)
The former will be the first inter-ontology links in the GO vocabularies and may cause errors with loading or parsing scripts that do not allow inter-ontology links. The addition of these links also has major implications for tools that ignore relationship types when summarizing annotations. For example, if your tool lumps annotations to kinase regulator activity together with the regulates parent kinase activity, users will retrieve gene products that function as kinase regulators (and not necessarily as kinases!) in a query for kinases.
A test file of the biological process-molecular function links is available from the GO website.
We plan to implement these links in the live ontology on November 30th, 2008. Please provide us with any feedback you might have regarding this plan.
EXP: Inferred from Experiment
A new evidence code, EXP, has been created for groups contributing high-quality manually-curated GO annotations from published experimental results, but who are unable to apply a specific experimental evidence code to each annotation. The EXP code is the parent code for the IDA, IPI, IMP, IGI and IEP experimental codes and can be used where any of the assays described by these codes is reported; however, we greatly encourage groups who annotate manually to GO to use one of the more specific experimental codes instead of EXP.
Currently EXP annotations are being supplied by the Reactome group, who have released almost 6,000 EXP annotations in the last month. As with all other manual evidence codes, EXP annotations are available via AmiGO and included in all downloadable files.
Further information is available in the evidence code documentation on the GO website.
Upcoming Meeting
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Yeast Genetics and Molecular Biology
July 22-27, 2008
University of Toronto, Ontario, Canada
Contact GO
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