Question: How do you use Biomart to get info about genes that didn't originate from Ensembl?
0
gravatar for ericbrenner
2.5 years ago by
ericbrenner0 wrote:

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

biomart ensembl genome • 730 views
ADD COMMENTlink modified 2.5 years ago by Jean-Karim Heriche21k • written 2.5 years ago by ericbrenner0
1

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>
ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Denise - Open Targets5.1k

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

ADD REPLYlink written 2.5 years ago by Emily_Ensembl20k
7
gravatar for Jean-Karim Heriche
2.5 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

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.

ADD COMMENTlink written 2.5 years ago by Jean-Karim Heriche21k
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