Genes Symbol Conversion not in biomaRt

Question

[bazok]

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

[Kevin Blighe]

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.

[bazok]

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

[GenoMax]

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

You can figure out the rest.

Answer 1

[Jean-Karim Heriche]

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.

Answer 2

[tamerg]

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.