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How to interpret MES ? #50

Closed Djoudjou2 closed 1 year ago

Djoudjou2 commented 1 year ago

Hello,

I have just a quick question about the event type "MES". Indeed, when I check with the NCBI database, the coordinates given by PSI-Sigma are for only one exon. Here an exemple : TNC - chr9:115046410-115046682.

How can I interpret that ?

Thanks in advance !

Juliette

wososa commented 1 year ago

Hi @Djoudjou2 ,

MES stands for multiple-exon splicing event. Do you mean that you only see one exon reported in the output file or there is only one alternative in the gene annotation? There should be more than 1 alternative exon in the event region if the event is reported as MES.

Best, Woody

Djoudjou2 commented 1 year ago

Thank you for your answer.

There is only one alternative exon in the gene annotation when I use the coordinates written in "Target Exon" (Chr9 : 115046410-115046682), and many exons (8 which can also be alternatively spliced!) when I use the coordinates written in "Event Region" (Chr9: 115042342-115073602)

I am a little bit confused for the interpretation of this event.

Thank you,

Juliette

wososa commented 1 year ago

The other alternative exons are not reported probably due to (1) coverage of the other exon is low or (2) the other exons are filtered by p-value or delta-PSI cutoff. Let me know this doesn’t answer your question.

Thanks, Woody

On Thu, Sep 21, 2023 at 10:49 AM Djoudjou2 @.***> wrote:

Thank you for your answer.

There is only one alternative exon in the gene annotation when I use the coordinates written in "Target Exon" (Chr9 : 115046410-115046682), and many exons (8 which can also be alternatively spliced!) when I use the coordinates written in "Event Region" (Chr9: 115042342-115073602)

I am a little bit confused for the interpretation of this event.

Thank you,

Juliette

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Djoudjou2 commented 1 year ago

Yes it answers my question.

Thank you very much !