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
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gpreising •
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
Hi Kevin,
That worked! I only lost 1.2K IDs with that package. Thanks so much for the help.
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Please provide examples of ID's that don't match. Using Entrezdirect may be possible in this case to get the info you want.
Sure, here are a few IDs that I could get gene names for but not RefSeq accressions
ENSDARG00000061451 ENSDARG00000061749 ENSDARG00000061764
Would the following link help? https://david.ncifcrf.gov/conversion.jsp