No gene name

Question

[rajdeepboral00]

Hello all,

I have used deseq for my data analysis on RNA seq and got a differential gene expression data on the corresponding ensembl ids, but then I used biomart to get the gene names, but some spaces are left blank for few ensembl ids, do all ensembl ids have their corresponding genes? when I searched for that ensembl id in internet also it shows no satisfactory result. What can be done in this case?

[ATpoint]

Does your annotation that was used for the count matrix creation match the version you use for biomaRt (Ensembl version)? See https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/accessing_ensembl.html#using-archived-versions-of-ensembl on how to let biomaRt know about the version and be sure you are using matched versions. Maybe the gene got dropped in recent Ensembl versions or was added recently?

[Ram]

Do you mean HGNC gene symbols?

Can you share a few examples of ENSG entries with no HGNC symbols please?

[rajdeepboral00]

ENSMUSG00000134655.1 ENSMUSG00000135994.1 ENSMUSG00000138963.1 Here are few examples of the ids that i didnt get any gene name. These are for mouse genome by the way.

[Dave Carlson]

Those are all long, non-coding RNA genes. Presumably they are computationally predicted, and likely there has not been enough work experimentally to provide more information about their functional effects. At the moment at least, there are no gene symbols associated with these genes.