Question: ENSEMBL annotation of genes start with "Gm" end with "Rik"
1
gravatar for SMILE
11 months ago by
SMILE130
SMILE130 wrote:

Dears,

When I did RNA-Seq and ChIP-Seq downstream analysis with GENE annotation of ENSEMBL. The final results are flooded with genes such as Gm's and Rik's. Based on Ensembl 'biotype' classifications in mouse, genes starting with 'Gm-' or ending with 'Rik' include protein-coding RNAs, long non-coding RNAs, and antisense transcripts.

Is it a proper way to filter out these genes before downstream analysis?

rna-seq chip-seq gene • 669 views
ADD COMMENTlink modified 11 months ago by Emily_Ensembl21k • written 11 months ago by SMILE130
3
gravatar for Emily_Ensembl
11 months ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

You could just use a RegEx if you're really keen to filter them. But they're real genes - we just don't know much about them yet.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Emily_Ensembl21k

Thank you Emily! It is good to know your opinions. How can I know more about the resources and evidence for these genes? Are they special annotations that are only included in ENSEMBL annotation not others?

ADD REPLYlink written 11 months ago by SMILE130
1

For any transcript you can look up the source of the annotation data. The Gm ones were originally annotated by MGI and the Rik ones by RIKEN.

ADD REPLYlink modified 11 months ago • written 11 months ago by Emily_Ensembl21k
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