[gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO.

[Jaak Vilo]

Hi,

Sorin Draghici wrote:
 > I'm just curious. How do you calculate the p-values without knowing the
 > set of genes these genes are coming from?

This is a relevant quetion, of course.

Having the whole universe of genes as the background would skew the 
results towards very broad (and hence somewhat useless) root categories.

In this case the background is the set of all genes annotated into the 
respective broad category. For example, all annotated genes for GO (in 
given species); all genes known to KEGG; or all genes known to Reactome.
Otherwise the comparisons would not be "fair".

But indeed, g:Profiler does not support a user-given background set.
For example, if one would like to study a strict subset of all 
transcription regulation related genes, then all broad categories of 
transcription regulation would be identified.

Another useful feature for end-users is that users are allowed to mix 
any supported ID-s freely in the same query.  Genes not known at all (or 
typos, for example) - would be identified as grey boxes. Unlike white 
boxes that correspond to known genes that have simply not been annotated 
to that same category [yet].

Cheers,

-Jaak

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