How do you use Biomart to get info about genes that didn't originate from Ensembl?

Question

[ericbrenner]

Hi, I've really liked using Biomart in the past, but I've recently realized that I don't know how to use it to get info on genes like this: http://www.ensembl.org/Gallus_gallus/Gene/Summary?db=otherfeatures;g=416764;r=15:25280-34065;t=XM_415059.5

which don't originate from Ensembl and don't have a formal ENS... ID. Is there a way to do it or do I have to find an alternative to Biomart? Thanks

[Denise CS]

No, don't go looking for an alternative to BioMart! It's such a great, easy to use tool. In addition to @Jean-Karim Heriche's answer, note that XMs are RefSeq mRNA predicted IDs. So that's the external reference ID you need to select. Also, leave the versioning out: so use XM_415059 but not XM_415059.5.

This is an example in XML:

<Dataset name = "ggallus_gene_ensembl" interface = "default" >
    <Filter name = "refseq_mrna_predicted" value = "XM_415059"/>
    <Attribute name = "ensembl_gene_id" />
    <Attribute name = "ensembl_transcript_id" />
    <Attribute name = "chromosome_name" />
    <Attribute name = "start_position" />
    <Attribute name = "end_position" />
    <Attribute name = "refseq_mrna_predicted" />
</Dataset>

[Emily]

Please do not cross-post to BioStars and StackExchange. https://bioinformatics.stackexchange.com/questions/2545/can-you-use-biomart-to-get-info-about-genes-that-didnt-originate-from-ensembl

Answer 1

[Jean-Karim Heriche]

In Ensembl's BioMart, you can input different types of gene IDs. Look under Filters > Gene > Input external references ID list [Max 500 advised]. The drop-down list shows the identifiers that are recognized. You can use it either to convert to Ensembl gene IDs or to get other info directly.