How to annotate gene ontologies based on Gene Symbols in R
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@dusanpetrovic-15081
Last seen 3.6 years ago
Switzerland

Hello Everyone,

I am looking for a straightforward way for associating gene ontologies (GO:...) to gene symbols (i.e. EIF1AY). I tried to use the GO.db package, but the latter does not seem to contain gene symbols, only gene ontologies

 

Thank you for your kind help

GO.db annotate • 520 views
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@james-w-macdonald-5106
Last seen 6 hours ago
United States
> library(Homo.sapiens)

> select(Homo.sapiens, "EIF1AY", "GOID", "SYMBOL")
'select()' returned 1:many mapping between keys and columns
  SYMBOL EVIDENCE ONTOLOGY       GOID
1 EIF1AY      IEA       MF GO:0003743
2 EIF1AY      IPI       MF GO:0005515
3 EIF1AY      IEA       BP GO:0006413
4 EIF1AY      IEA       MF GO:0043023
>
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Or maybe you wanted to go the other way?

> gos <- head(keys(Homo.sapiens, "GOID"))
> gos
[1] "GO:0000001" "GO:0000002" "GO:0000003" "GO:0000006" "GO:0000007"
[6] "GO:0000009"
> mapIds(Homo.sapiens, gos, "SYMBOL","GOID", multiVals = "list")
'select()' returned 1:many mapping between keys and columns
$`GO:0000001`
[1] NA

$`GO:0000002`
 [1] "SLC25A4"  "TYMP"     "MEF2A"    "MPV17"    "OPA1"     "LONP1"   
 [7] "AKT3"     "SLC25A36" "MRPL17"   "PIF1"     "SLC25A33" "MGME1"   

$`GO:0000003`
[1] "MMP23B"

$`GO:0000006`
[1] NA

$`GO:0000007`
[1] NA

$`GO:0000009`
[1] "ALG12"

 

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@dusanpetrovic-15081
Last seen 3.6 years ago
Switzerland

Awesome James, your first response was exactly what I wanted

Thank you so much

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