Why we do the differential splicing anlysis

[Alienhuo]

Recently, I am working on a presentation. The topic is the differential splicing analysis. I still not very clear why we need to do the analysis on the differential splicing. Right now, we already got the diff expression gene, what the relationship of the diff expression genes and the diff transcripts?

Thank you in advance.

[Bukowski]

Not all transcripts of a gene will be diferentially regulated in the same way. Gene level summarisation is crude, and best left in the past along with microarrays..

I have a great example I show people where I have a gene with two transcripts that at the gene level doesn't change expression between conditions. However there's a complete change between the transcript level expression, one is downregulated completely, the other is upregulated. Completely missed at the gene level.

[dpryan]

As Bukowski alluded, a gene can be expressed at the same level, but if a different splice variant is being expressed then it's possible that its function or subcellular localization are changed. Of course there are a couple difficulties encountered when dealing with transcript level analyses. Firstly actually detecting transcript-level changes is often quite difficult (cufflinks et al. try), as opposed to gene or exon-level changes, which are a bit more straight-forward. Secondly, assuming you can confidently find differential splicing, the real hard part is reliably coming up with what, if anything, it might mean. Unless you're looking at a well studied gene, the various splice forms are probably unstudied, so it's completely unclear what to even make of a finding.

[Alienhuo]

Thank you, guys.

[Cofactor Genomics]

Agreed with Bukowski and dpryan,
What I have seen over a number of studies is that in order to characterize at the isoform level (and be confident) additional sequencing/coverage is necessary. This relates to the aspect that you are trying to characterize the regions of the transcripts that are unique between isoforms and compare that representation. If you are not taking an isoform approach, more often than not it will be other members in the same pathway that show up in the differential expression analysis (assuming the change is in a pathway).


Jarret Glasscock
Cofactor Genomics

http://cofactorgenomics.com

http://www.linkedin.com/in/jarretglasscock

[Alienhuo]

Thank you, Cofactor Genomics.

[chadn737]

As Bukowski alluded, a gene can be expressed at the same level, but if a different splice variant is being expressed then it's possible that its function or subcellular localization are changed. Of course there are a couple difficulties encountered when dealing with transcript level analyses. Firstly actually detecting transcript-level changes is often quite difficult (cufflinks et al. try), as opposed to gene or exon-level changes, which are a bit more straight-forward. Secondly, assuming you can confidently find differential splicing, the real hard part is reliably coming up with what, if anything, it might mean. Unless you're looking at a well studied gene, the various splice forms are probably unstudied, so it's completely unclear what to even make of a finding.

My emphasis added.