other

Other general questions about the Gene Ontology and its products.

Reporting GO slim results, why shouldn't I display my "GO slim" results as a pie chart ?

The numbers provided by a GO slim are an annotation count not a gene product count, and so gene products may be present in more than one bin. Therefore displaying GO slim totals as percentages is not meaningful. For your results to be interpreted fully, you should also report how many genes are annotated but not in your slim, and how many genes do not slim.

What is "GO slimming" ?

Mapping granular annotations of a set of genes to one or more high-level, broader parent terms is referred to as "GO slimming". GO slimming is commonly used to report an overview of a genome or to a set of summarize experimental results. GO hosts a number of predefined Slim sets, a generic GO slim, and a number of slims tailored to give good coverage for some well studied/annotated model species.

How do I create a user defined "GO slim"?

GO hosts a number of predefined Slim sets, a generic GO slim, and a number of slims tailored to give good annotation coverage for some well studied/annotated model species. The available GO slimming tools also provide an option to upload your own term set. For most applications you usually need to adjust the terms in the slim to represent your results (i.e to reduce the number of terms, or to replace terms in regions of special interest with more specific children). The generic GO slims or organism specific slims are a good starting point to create your own GO slim.