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[gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO.
vilo at quretec.com
Fri Oct 5 14:01:36 PDT 2007
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].
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