[miso-users] Events with many gene annotations

[Tyler Funnell]

Hi Yarden,

Yes that's right. The problem is most noticeable for the ALE/AFE events for the reason you mentioned, but I think the current event to gene mapping could have improper annotations for other event types as well. For example, small genes that exist within the introns in a SE event would be picked up.

Cheers,
Tyler


On Aug 28, 2013, at 2:03 PM, Yarden Katz <yarden at mit.edu> wrote:

> Hi Tyler,
> 
> Some of the AFE/ALE annotations, which we are currently reworking, have span very large genomic coordinates as you noted.  I believe these are probably dubious/faulty annotations.  But in any case, as you say, if you overlap the outer-most coordinates with genes there will potentially be many overlapping genes.
> 
> If I understand correctly, you're proposing to merge the first exon with all genes, then the second exon will genes, and take the intersection of those? 
> 
> Best, --Yarden
> 
> On Aug 27, 2013, at 10:31 PM, Tyler Funnell wrote:
> 
>> Hello,
>> 
>> I've noticed that for some alternative events, there are many gene annotations in the event to ensembl Id mapping file. For example AFE event 83896 at uc002kgt.1@uc002hvt.1 has quite a few. I think this might be because the left-most and right-most coordinates for this particular event cover a large section of the chromosome and the gene mappings are based on these coordinates. If I'm right, I think a better way would be to get the overlap between genes (or gene exons) and individual event exons first, then merge to the event level.
>> 
>> Thank you,
>> Tyler
>> 
>> 
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