Question: Genes Symbol Conversion not in biomaRt
0
gravatar for bazok
8 weeks ago by
bazok0
bazok0 wrote:

Hi All, Please I have a list of gene symbols that I want to convert to ensembl ID. I have used biomart, ucsc and Org.Hs.eg.db, "NA" was returned. However, random checking them on genecard, i could get the ensembl ID. As the list is around 2.5k genes, I was wondering if there are other highly recommended db for missing genes on biomaRt and Org.Hs.eg.db

Thanks alot

rna-seq gene • 183 views
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by bazok0

This is a continuation of this thread, correct? - Conversion of Gene Name to Ensembl ID

Which genes are being returned as NA? - can you provide some examples, please.

ADD REPLYlink written 8 weeks ago by Kevin Blighe60k

Hi Kevin, Correct. Some of the genes are AAED1 AARS AATK-AS1 AC093375.1 ACN9 ACPT LINC00152 LINC00162 LINC00176 KIAA0922 KIAA0947 ZNF788 ZNF812 ZNF818P ZNRD1-AS1 ZUFSP

Thanks

ADD REPLYlink written 8 weeks ago by bazok0

ZUFSP is an old alias for current gene name ZUP1.
TMEM131L is new name for KIAA0922 gene.

You can figure out the rest.

ADD REPLYlink written 8 weeks ago by genomax83k
2
gravatar for Jean-Karim Heriche
8 weeks ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k wrote:

You should try the Ensembl perl API. It is much more flexible than the REST API or Biomart. In particular, look at methods such as get_all_DBLinks() and get_all_synonyms(). If working with HGNC gene symbols, you can download a table mapping symbols to IDs from the HGNC web site. Make sure to select the Alias and previous names/symbols columns to get synonyms and previously used symbols.

ADD COMMENTlink written 8 weeks ago by Jean-Karim Heriche22k
1
gravatar for tamerg
8 weeks ago by
tamerg70
tamerg70 wrote:

For alternative to the biomaRt and Org.Hs.eg.db check out the biobtree. It resolved all the genes you mentioned except AC093375.1 which doesn't seem to belong to an ensembl ID.

ADD COMMENTlink written 8 weeks ago by tamerg70
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