Question: org.Hs.eg.db does not rerieve all existing records
0
gravatar for antonvila.s
4.7 years ago by
Spain
antonvila.s0 wrote:

Hi,

when I use org.Hs.eg.db to retrieve gene names with keytype = ËNSEMBL", I get incomplete lists. For example

> query
 [1] "ENSG00000201291" "ENSG00000206687" "ENSG00000212402" "ENSG00000231747" "ENSG00000239935" "ENSG00000241482"
 [7] "ENSG00000243053" "ENSG00000243588" "ENSG00000251811" "ENSG00000254713"

> GENEINFO <- select(org.Hs.eg.db, keys=query, columns=c("ENSEMBL","SYMBOL","GENENAME", "UNIGENE"), keytype="ENSEMBL")

results in

> GENEINFO
           ENSEMBL   SYMBOL                           GENENAME   UNIGENE
1  ENSG00000201291     <NA>                               <NA>      <NA>
2  ENSG00000206687     <NA>                               <NA>      <NA>
3  ENSG00000212402 SNORA74B small nucleolar RNA, H/ACA box 74B Hs.692720
4  ENSG00000231747     <NA>                               <NA>      <NA>
5  ENSG00000239935     <NA>                               <NA>      <NA>
6  ENSG00000241482     <NA>                               <NA>      <NA>
7  ENSG00000243053     <NA>                               <NA>      <NA>
8  ENSG00000243588     <NA>                               <NA>      <NA>
9  ENSG00000251811     <NA>                               <NA>      <NA>
10 ENSG00000254713     <NA>                               <NA>      <NA>

However, I can easily check online that ENSG00000201291 has

Approved symbol: RNU1-34P

Approved name: RNA, U1 small nuclear 34, pseudogene

(http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:48376)

why am I not getting these records with the org.Hs.eg.db package?

best,

Antón

 

 

 

org.hs.eg.db • 702 views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by antonvila.s0
Answer: org.Hs.eg.db does not rerieve all existing records
0
gravatar for James W. MacDonald
4.7 years ago by
United States
James W. MacDonald51k wrote:

It's because the org.Hs.eg.db package is based on Entrez Gene IDs, rather than Ensembl. If you want to annotate starting with Ensembl IDs, you are likely better off using biomaRt instead:

> library(biomaRt)
> query <- c("ENSG00000201291", "ENSG00000206687", "ENSG00000212402", "ENSG00000231747", "ENSG00000239935", "ENSG00000241482",
+            "ENSG00000243053", "ENSG00000243588", "ENSG00000251811", "ENSG00000254713")
> mart <- useMart("ensembl","hsapiens_gene_ensembl")

> getBM(c("ensembl_gene_id","hgnc_symbol","external_gene_name","unigene"), "ensembl_gene_id", query, mart)
  ensembl_gene_id hgnc_symbol external_gene_name   unigene
1 ENSG00000201291    RNU1-34P           RNU1-34P          
2 ENSG00000206687   RNU1-109P          RNU1-109P          
3 ENSG00000212402    SNORA74B           SNORA74B Hs.692720
4 ENSG00000231747                     AC079922.2          
5 ENSG00000243053    RPL31P58           RPL31P58          
6 ENSG00000251811                          Y_RNA          
7 ENSG00000254713  HNRNPA1P72         HNRNPA1P72    
ADD COMMENTlink written 4.7 years ago by James W. MacDonald51k
Answer: org.Hs.eg.db does not rerieve all existing records
0
gravatar for antonvila.s
4.7 years ago by
Spain
antonvila.s0 wrote:

It works! thanks for your answer.

ADD COMMENTlink written 4.7 years ago by antonvila.s0
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