[BioC] Genes and their associated GO terms and pathways

[Wolfgang Huber]

Daren Tan ha scritto:
> I have a set of differentially expressed genes, and want to know what are their GO terms, and pathway that they reside in. I have installed GO.db and KEGG.db, but unsure how to get started. 
>  
> For examples, genes <- c("TP53", "SOX4", "PTEN"), whats next ?
> 
>

Hi Daren

library("org.Hs.eg.db")
genes <- c("TP53", "SOX4", "PTEN")

entrez = toTable( revmap(org.Hs.egSYMBOL)[genes] )
go = toTable( org.Hs.egGO[entrez$gene_id] )
combined = merge(entrez, go)


 > combined
    gene_id symbol      go_id Evidence Ontology
1     5728   PTEN GO:0000079      TAS       BP
2     5728   PTEN GO:0001525      IEA       BP
3     5728   PTEN GO:0006470      IDA       BP

         . . . .

91    7157   TP53 GO:0019899      IPI       MF
92    7157   TP53 GO:0046982      IPI       MF
93    7157   TP53 GO:0047485      IPI       MF



Best wishes
      Wolfgang

 > sessionInfo()
R version 2.9.0 Under development (unstable) (2008-11-27 r47025)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices datasets  utils     methods
[8] base

other attached packages:
[1] org.Hs.eg.db_2.2.6  RSQLite_0.7-1       DBI_0.2-4
[4] AnnotationDbi_1.5.6 Biobase_2.3.3       fortunes_1.3-5

----------------------------------------------------
Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber