Question

How to annotate gene ontologies based on Gene Symbols in R

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dusan.petrovic • 0

@dusanpetrovic-15081

Last seen 6.7 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 • 1.3k views

ADD COMMENT • link 6.7 years ago dusan.petrovic • 0

score 0 · Answer 1 · 2018-03-05

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 7 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
>

ADD COMMENT • link 6.7 years ago James W. MacDonald 67k

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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"

ADD REPLY • link 6.7 years ago James W. MacDonald 67k

score 0 · Answer 2 · 2018-03-06

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dusan.petrovic • 0

@dusanpetrovic-15081

Last seen 6.7 years ago

Switzerland

Awesome James, your first response was exactly what I wanted

Thank you so much

ADD COMMENT • link 6.7 years ago dusan.petrovic • 0