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Question: dexseq doesn't identify exons as differential
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gravatar for Assa Yeroslaviz
6 days ago by
Assa Yeroslaviz1.3k
Munich, Germany
Assa Yeroslaviz1.3k wrote:

hi, 

I was wondering how dexseq is calculating the differential exon usage. I am having troubles interpreting the results, which I think are significant, but dexseq does not :-)

I have here one of the genes from my run, which looks to me, that it is very much differentially used. the three plots are the results for the counts, the expression and the splicing events calculated by DEXSeq. 

I don't understand the results. To my eyes, it looks as if the counts of exons 26-60 should be differentially expressed, but somehow they're not. On the other hand, the two exon defined as different are exons 17 and 19, which doesn't look at all changed.

counts:

counts

expression:

expression

splicing: here it looks completely different than the other two plots.

splicing

Is there an explanation to that?

thanks

Assa

ADD COMMENTlink modified 6 days ago by mat.lesche10 • written 6 days ago by Assa Yeroslaviz1.3k

the link to the images, if needed are added:

https://s26.postimg.org/rzjgcfd8p/splicing.png

https://s26.postimg.org/6rad8qo5l/counts.png

https://s26.postimg.org/5qa4jm761/expression.png

 

ADD REPLYlink modified 6 days ago • written 6 days ago by Assa Yeroslaviz1.3k
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gravatar for mat.lesche
6 days ago by
mat.lesche10
Germany
mat.lesche10 wrote:

Hi Assa,

DEXSeq doesn't look for differential expression. The tool is designed to look for a differential usage of single exon bins compared to the usage of all other exon bins in a gene. In your case the gene shows an over expression in EB2 compared to the other condition. Hence the high expression in EB2 is normal, except for the two exon bins 17 and 19. Here expression/usage is not on the same level as compared to the other exons. That's why they are marked as significant. The concept of usage is completely different to expression and takes a while to wrap one's head around it. Actually here, DEXSeq Usage and Expression Confusion is a very good example, explained by Simon Anders. That should make things quite clear

best

mathias

ADD COMMENTlink written 6 days ago by mat.lesche10

Hi thanks for the explanation and the link. I think I have understood what the goal of DEXSeq, but than again it still doesn't do what you say, at least not for all the exons. In the gene I have shown above there are almost two separate parts to the gene. (From the biological side, there is an alternative promotor in the region of exon (bin) 26. This is why the change of read counts is so clear. )

But what I don;t understand about the assignment of significant exon bins is that there are also other exon bins with similar behavior before exon 26. So why these two exons? Even these two are not really similar in their expression behavior or count pattern.

Is there a reason why these two suppose to be significant, while other not?

ADD REPLYlink written 2 days ago by Assa Yeroslaviz1.3k
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