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How to map ENSEMBL Transcript IDs to coding/non-coding/miRNA

I have microarray gene expression data obtained from Affymetrix HTA 2.0. Using the annotation file, I was able to map the transcript clusters IDs (e.g. TC21000363.hg) to ENSEMBL Transcript IDs (e.g. ENST00000399889).

Now, I would like to know, whether the ENSEMBL Transcript IDs represent: - coding mRNA - non-coding RNA - miRNA

I have tried Biomart for this, but with no success, because Biomart does not allow for this kind of classification.

Would appreciate any help!

rna-seq mapping microarray gene expression hta
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updated by Biostar Biostar • written by SunRise2019 • SunRise2019

1 answer

Biomart does not allow for this kind of classification.

I think it does.

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >

    <Dataset name = "hsapiens_gene_ensembl" interface = "default" >
        <Filter name = "ensembl_transcript_id" value = "ENST00000399889"/>
        <Attribute name = "ensembl_transcript_id" />
        <Attribute name = "transcript_biotype" />
    </Dataset>
</Query>

Transcript stable ID,Transcript type
ENST00000399889,protein_coding
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written by Pierre Lindenbaum Pierre Lindenbaum

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