[BioC] GO IDs to Terms (in Globaltest)

[James W. MacDonald]

Hi Tarun,

Tarun Nayar wrote:
> Hi,
>  
> I've output a 'gt.result' in a globaltest analysis of a microarray
> experiment. This is a class with a number of slots summarizing the
> results of a globaltest on a number of genesets. In this experiment I
> tested the association of a number of GO IDs with gene expression. I'd
> like to convert these IDs to GO Terms for ease of interpretation.
>  
>                  Genes Tested Statistic Q Expected Q sd of Q   P-value
> FDR.adjusted
> GO:0008318     5      5      36.929     5.6901  5.0507 0.0010123
> 0.70613
> GO:0018344     3      3      53.234     5.2187  7.0999 0.0011494
> 0.70613
> GO:0018348     3      3      53.234     5.2187  7.0999 0.0011494
> 0.70613
> 
> The method to convert KEGG Pathway IDs to KEGG Pathway Names is as
> follows (for a 'gt.result' called "top20_k")
>  
> 
>>names(top20_k) <- as.list(KEGGPATHID2NAME)[names(top20_k)]
> 
>  
> Is there a similar command to convert GO IDs in this context?

 > library(GO)
 > library(annotate)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

     Vignettes contain introductory material. To view, type
     'openVignette()' or start with 'help(Biobase)'. For details
     on reading vignettes, see the openVignette help page.


 > gos <- ls(GOTERM)[5:15]
 > gos
  [1] "GO:0000006" "GO:0000007" "GO:0000009" "GO:0000010" "GO:0000011"
  [6] "GO:0000012" "GO:0000014" "GO:0000015" "GO:0000016" "GO:0000017"
[11] "GO:0000018"
 > sapply(mget(gos, GOTERM), Term)
                                                    GO:0000006
              "high affinity zinc uptake transporter activity"
                                                    GO:0000007
                  "low-affinity zinc ion transporter activity"
                                                    GO:0000009
                      "alpha-1,6-mannosyltransferase activity"
                                                    GO:0000010
                   "trans-hexaprenyltranstransferase activity"
                                                    GO:0000011
                                         "vacuole inheritance"
                                                    GO:0000012
                                  "single strand break repair"
                                                    GO:0000014
"single-stranded DNA specific endodeoxyribonuclease activity"
                                                    GO:0000015
                           "phosphopyruvate hydratase complex"
                                                    GO:0000016
                                            "lactase activity"
                                                    GO:0000017
                                   "alpha-glucoside transport"
                                                    GO:0000018
                             "regulation of DNA recombination"

Best,

Jim


>  
> Thanks
>  
> Tarun Nayar
> Genome Sciences Centre
> Vancouver, BC
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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