[BioC] Understanding GOstats

[James W. MacDonald]

Hi Alex,

alex lam (RI) wrote:
> Dear colleagues,
> 
> I would like to check if my understanding onone aspect of GOstats is
> correct.
> 
> The probeset 1370428_x_at is linked to the GO term GO:0002474
> 
> When I use hyperGTest (with conditional=F), if this probeset is DE,
> enrichment of GO:0002474 will be tested. And so will its parent GO term
> GO:0048002, even this GO term is not explicitly linked to the affy id in
> the annotation. Is that correct? GOstats will follow the GO tree from
> bottom-up to conduct tests?

Yes. Although this particular probeset isn't mapped directly to the 
parent GO term, it _is_ by definition mapped to that term since the 
child term is a subset of the parent (here subset being defined by 
either an is_a or a part_of relationship to the parent).

Note that this will be true even if conditional = TRUE, unless 
GO:0002474 is significant _and_ that particular probeset contributed to 
that significance. Although we shouldn't be talking about probesets here 
because the GO analysis is done on the gene level.

> 
> On a slightly different matter, the grandparent node of GO:0002474,
> GO:0019882, is explicitly linked to this affy id in the annotation. Why
> is this so, but not the parent node GO:0048002?

Good question, but wrong forum. We just repackage existing annotations, 
and as far as I can tell everybody says the same thing about this gene. 
For instance, NCBI:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=24737

The same thing is true of Affy and Ensembl.

Best,

Jim


> 
> Many thanks,
> Alex
> 
> --------------------------------------------
> Alex C. Lam
> Roslin Institute (Edinburgh)
> Midlothian
> EH25 9PS
> United Kingdom
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
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