Zebrafish Ensembl gene ID to RefSeq protein accession?

Question

[gpreising]

Hi,

I am trying to convert zebrafish Ensembl gene IDs to RefSeq protein accessions. I did this partially with BioMart, but only got ~12k RefSeq accessions for the ~22k Ensembl IDs I queried. Are there any other tools available that I could use to convert the remaining ~10k Ensembl gene IDs, ideally ones that folks have used for zebrafish? From my google searches I can see that most of these are optimized for rat/mouse/human.

Thanks,
Gabe

[GenoMax]

Please provide examples of ID's that don't match. Using Entrezdirect may be possible in this case to get the info you want.

[gpreising]

Sure, here are a few IDs that I could get gene names for but not RefSeq accressions

ENSDARG00000061451 ENSDARG00000061749 ENSDARG00000061764

[Sishuo Wang]

Would the following link help? https://david.ncifcrf.gov/conversion.jsp

Answer 1

[Kevin Blighe]

You can try the org.Dr.eg.db package - it may match more IDs for you:

library(org.Dr.eg.db)

ens <- c('ENSDARG00000061451', 'ENSDARG00000061749',
  'ENSDARG00000061764')

keytypes(org.Dr.eg.db)

 [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
 [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
[11] "GO"           "GOALL"        "IPI"          "ONTOLOGY"     "ONTOLOGYALL" 
[16] "PATH"         "PFAM"         "PMID"         "PROSITE"      "REFSEQ"      
[21] "SYMBOL"       "UNIGENE"      "UNIPROT"      "ZFIN"

.

mapIds(org.Dr.eg.db, keys = ens,
  column = c('REFSEQ'), keytype = 'ENSEMBL')

'select()' returned 1:many mapping between keys and columns
ENSDARG00000061451 ENSDARG00000061749 ENSDARG00000061764 
    "NM_001079967"                 NA     "XM_005173182"


select(org.Dr.eg.db, keys = ens,
  columns = c('REFSEQ',  'ENTREZID', 'SYMBOL', 'ENSEMBL'),
  keytype = 'ENSEMBL')

'select()' returned 1:many mapping between keys and columns
              ENSEMBL       REFSEQ ENTREZID SYMBOL
1  ENSDARG00000061451 NM_001079967   558048  n4bp2
2  ENSDARG00000061451 NP_001073436   558048  n4bp2
3  ENSDARG00000061451 XM_021475000   558048  n4bp2
4  ENSDARG00000061451 XP_021330675   558048  n4bp2
5  ENSDARG00000061749         <NA>     <NA>   <NA>
6  ENSDARG00000061764 XM_005173182   559276  ahnak
7  ENSDARG00000061764 XM_005173183   559276  ahnak
8  ENSDARG00000061764 XM_005173184   559276  ahnak
9  ENSDARG00000061764 XM_005173188   559276  ahnak
10 ENSDARG00000061764 XM_009291066   559276  ahnak
11 ENSDARG00000061764 XM_017359122   559276  ahnak
12 ENSDARG00000061764 XM_021481163   559276  ahnak
13 ENSDARG00000061764 XM_021481164   559276  ahnak
14 ENSDARG00000061764 XP_005173239   559276  ahnak
15 ENSDARG00000061764 XP_005173240   559276  ahnak
16 ENSDARG00000061764 XP_005173241   559276  ahnak
17 ENSDARG00000061764 XP_005173245   559276  ahnak
18 ENSDARG00000061764 XP_009289341   559276  ahnak
19 ENSDARG00000061764 XP_017214611   559276  ahnak
20 ENSDARG00000061764 XP_021336838   559276  ahnak
21 ENSDARG00000061764 XP_021336839   559276  ahnak

Kevin

[gpreising]

Hi Kevin,

That worked! I only lost 1.2K IDs with that package. Thanks so much for the help.