[BioC] topGO spurious GO terms?

[Jan Kim]

On Tue, Dec 17, 2013 at 05:35:49AM -0800, Adam [guest] wrote:
> 
> I am using topGO's custom workflow to get enrichment of GO terms. In
> my top 20 nodes there are significant GO terms that are not found in my
> "universe". I am new to analyzing GO information and I can only assume
> that these spurious GO IDs are part of pathways of GO IDs in my universe
> and are significant by association? Alternatively, topGO has a more
> updated list of GO IDs and has substituted the names in my universe. Any
> advice would be greatly appreciated!

this is likely a (desired!) effect of the multiple inheritance
structure of the gene ontologies -- remember / notice that ontologies
are directed acyclic graphs in which each term has at least one
parent term which is more general. This is mostly analogous to the
"is-a" relationships used in class hierarchies (of object oriented
programming), e.g. "gene expression" is a (more specific type of)
"macromolecular metaboloc process", which is a "metabolic process",
which is a "biological process". So if (say) a transcription factor
encoding gene is annotated with "gene expression", it is implicitly
also annotated with all the other (parent, grandparent etc.) terms,
which you may perceive to be "spurious".

Best regards, Jan

> 
> 
>  -- output of sessionInfo(): 
> 
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
> 
> attached base packages:
> [1] parallel  grid      stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
>  [1] topGO_2.12.0         SparseM_1.03         GO.db_2.9.0          RSQLite_0.11.4       DBI_0.2-7            AnnotationDbi_1.22.6 Biobase_2.20.1       BiocGenerics_0.6.0  
>  [9] graph_1.38.3         ggplot2_0.9.3.1     
> 
> loaded via a namespace (and not attached):
>  [1] colorspace_1.2-4   dichromat_2.0-0    digest_0.6.3       gtable_0.1.2       IRanges_1.18.4     labeling_0.2       lattice_0.20-24    MASS_7.3-29        munsell_0.4.2     
> [10] plyr_1.8           proto_0.3-10       RColorBrewer_1.0-5 reshape2_1.2.2     scales_0.2.3       stats4_3.0.1       stringr_0.6.2      tools_3.0.1       
> 
> 
> --
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> 
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-- 
 +- Jan T. Kim -------------------------------------------------------+
 |             email: jttkim at gmail.com                                |
 |             WWW:   http://www.jtkim.dreamhosters.com/              |
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