<p>I guess the following code will help,</p>

<pre><code>source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")
library("biomaRt")
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
#listAttributes(ensembl)
mapping &lt;- getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "go_id"), mart = ensembl)
head(mapping)
</code></pre>

CC BY-SA 3.0
2017-09-18T19:22:43.573Z
2017-09-18T19:40:03.890Z
2017-09-18T19:40:03.890Z
arup
<p>Here's an example for the mouse genome:</p>

<pre class="lang-r prettyprint-override"><code>library(org.Mm.eg.db)
select(org.Mm.eg.db, c("GO:0048406"), c("GENENAME","SYMBOL"), c("GO"))
</code></pre>

<p>You get output like:</p>

<pre><code>                                                    GENENAME SYMBOL
1                                     pregnancy zone protein    Pzp
2 nerve growth factor receptor (TNFR superfamily, member 16)   Ngfr
3 nerve growth factor receptor (TNFR superfamily, member 16)   Ngfr
4                                             neurotrophin 3   Ntf3
5             neurotrophic tyrosine kinase, receptor, type 1  Ntrk1
6            furin (paired basic amino acid cleaving enzyme)  Furin
7              proprotein convertase subtilisin/kexin type 6  Pcsk6
8                                                 sortilin 1  Sort1
9                                      alpha-2-macroglobulin    A2m
</code></pre>

<p><strong>Edit</strong>: Given your comment that you want instead a list of all genes with a GO term associated with them (for human):</p>

<pre><code>library(org.Hs.eg.db) # Install it from bioconductor yourself
unlist(as.list(org.Hs.egSYMBOL)[mappedkeys(org.Hs.egGO)])
</code></pre>

<p>The <code>mappedkey()</code> part gets the index into the bimap of all entries with a valid GO mapping. That's then used to subset the symbol bimap (after converting to a list).</p>

CC BY-SA 3.0
2017-09-18T17:05:28.830Z
2017-09-18T20:38:20.467Z
2017-09-18T20:38:20.467Z
Devon Ryan
<p>I need a command in R to retrieve all human genes associated with a Gene Ontology entry. I tried to look for it online but did not find it.</p>

CC BY-SA 3.0
2017-09-20T07:06:33.550Z
@DanielStandage I am not sure this question is about the human genome.
llrs
CC BY-SA 3.0
2017-09-20T16:15:46.077Z
@Llopis When he says "retrieve all human genes" it definitely makes *me* think of the human genome. :-)
Daniel Standage
CC BY-SA 3.0
2017-09-20T16:18:40.570Z
@Daniel yes, but the question is not about the human genome. Or should we also use gene as tag here ? Maybe we use different definitions of the tag
llrs
<r><human-genome><gene-ontology>
Retrieving a list of human genes having GO associations
# Retrieving a list of human genes having GO associations

(Asked by: username_0 on 2017-09-18)

I need a command in R to retrieve all human genes associated with a Gene Ontology entry. I tried to look for it online but did not find it.

**Tags:** r, human-genome, gene-ontology
> **Comments:**
> **username_1**: @DanielStandage I am not sure this question is about the human genome.  
> **username_2**: @Llopis When he says "retrieve all human genes" it definitely makes *me* think of the human genome. :-)  
> **username_1**: @Daniel yes, but the question is not about the human genome. Or should we also use gene as tag here ? Maybe we use different definitions of the tag  

---

## 2 answers

### Answer by username_3 on 2017-09-18. Score: 6

I guess the following code will help,
source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")
library("biomaRt")
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
#listAttributes(ensembl)
mapping <- getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "go_id"), mart = ensembl)
head(mapping)


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### Answer by username_4 on 2017-09-18. Score: 6

Here's an example for the mouse genome:
library(org.Mm.eg.db)
select(org.Mm.eg.db, c("GO:0048406"), c("GENENAME","SYMBOL"), c("GO"))

You get output like:
                                                    GENENAME SYMBOL
1                                     pregnancy zone protein    Pzp
2 nerve growth factor receptor (TNFR superfamily, member 16)   Ngfr
3 nerve growth factor receptor (TNFR superfamily, member 16)   Ngfr
4                                             neurotrophin 3   Ntf3
5             neurotrophic tyrosine kinase, receptor, type 1  Ntrk1
6            furin (paired basic amino acid cleaving enzyme)  Furin
7              proprotein convertase subtilisin/kexin type 6  Pcsk6
8                                                 sortilin 1  Sort1
9                                      alpha-2-macroglobulin    A2m

Edit: Given your comment that you want instead a list of all genes with a GO term associated with them (for human):
library(org.Hs.eg.db) # Install it from bioconductor yourself
unlist(as.list(org.Hs.egSYMBOL)[mappedkeys(org.Hs.egGO)])

The mappedkey() part gets the index into the bimap of all entries with a valid GO mapping. That's then used to subset the symbol bimap (after converting to a list).


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