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Genes Symbol Conversion not in biomaRt

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

gene rna-seq
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written by bazok • 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

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written by bazok • bazok

2 answers

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.

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written by Jean-Karim Heriche Jean-Karim Heriche

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.

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written by tamerg tamerg

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