[BioC] How to retrieve all GO terms at level 5 as well as their annotated genes

[Zadeh, Jenny Drnevich]

Hi Peter,

I recently went through this with a client and he had a hard time understanding that there is not really a unique "level" of GO terms. Many of your level 5 terms can also be level 4 terms, or level 3 terms or level 6 term, etc. This is due the acyclic nature of the GO terms and the multiple paths possible from one ancestor to one descendent. Just want to point this out!

Cheers,
Jenny 

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Hervé Pagès
Sent: Monday, June 24, 2013 8:20 PM
To: Peter Davidsen
Cc: bioconductor at r-project.org
Subject: Re: [BioC] How to retrieve all GO terms at level 5 as well as their annotated genes

Hi Peter,

Probably not the most elegant way, but you could do something like this (granted that I understand correctly what a "level 5" term is):

   library(GO.db)

   getAllBPChildren <- function(goids)
   {
     ans <- unique(unlist(mget(goids, GOBPCHILDREN), use.names=FALSE))
     ans <- ans[!is.na(ans)]
   }

   level1_BP_terms <- getAllBPChildren("GO:0008150")     # 23 terms
   level2_BP_terms <- getAllBPChildren(level1_BP_terms)  # 256 terms
   level3_BP_terms <- getAllBPChildren(level2_BP_terms)  # 3059 terms
   level4_BP_terms <- getAllBPChildren(level3_BP_terms)  # 9135 terms
   level5_BP_terms <- getAllBPChildren(level4_BP_terms)  # 15023 terms

   library(org.Hs.eg.db)
   level5_genes <- mget(intersect(level5_BP_terms, keys(org.Hs.egGO2EG)),
                        org.Hs.egGO2EG)

Cheers,
H.

On 06/21/2013 02:28 AM, Peter Davidsen wrote:
> Dear list,
>
> I'm looking for a way to get the names of all Gene Ontology terms for 
> Biological Processes at level 5 as well as the genes (human gene
> symbols) annotated to each of the level 5 GO terms.
>
> I have tried to query the DAVID knowledgebase, but the online tool 
> doesn't seem to respond to any requests. Hence, could anybody maybe 
> point me in the direction of a package that could provide me with the 
> same information?
>
> Kind regards,
> Peter
>
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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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