Question: How to annotate gene ontologies based on Gene Symbols in R
0
gravatar for dusan.petrovic
15 months ago by
Switzerland
dusan.petrovic0 wrote:

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

annotate go.db • 278 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by dusan.petrovic0
Answer: How to annotate gene ontologies based on Gene Symbols in R
0
gravatar for James W. MacDonald
15 months ago by
United States
James W. MacDonald50k wrote:
> 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 COMMENTlink written 15 months ago by James W. MacDonald50k

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 REPLYlink written 15 months ago by James W. MacDonald50k
Answer: How to annotate gene ontologies based on Gene Symbols in R
0
gravatar for dusan.petrovic
15 months ago by
Switzerland
dusan.petrovic0 wrote:

Awesome James, your first response was exactly what I wanted

Thank you so much

ADD COMMENTlink written 15 months ago by dusan.petrovic0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 174 users visited in the last hour