[miso-users] Is exon-centric Psi always referring to isoform A?

[Yarden Katz]

Hi,

Whether the Psi value corresponds to the long or short isoform (in the case of two isoform events) is arbitrary, but by convention MISO uses the first isoform that appears in the GFF file.  In our own GFF files that are listed on the website, we've ordered it so that the longer of the two isoforms appear first.  Therefore, in the case of an SE event, the Psi value is by convention the percent inclusion of the exon as opposed to percent exclusion.  If you run MISO on a GFF file other than ours, it will just do it based on the order of appearance of mRNA entries for your event in the file.  Note that GFF files are inherently unordered, so our interpretation of the ordering is just for convenience.

To avoid confusion, your MISO output contains a field called "isoforms" that gives a comma-separated list of isoforms (using their ID= values from the GFF file).  In the two isoforms case, the first mRNA in the "isoforms" field is the one with the value Psi, and the second one listed is 1-Psi.

  --Yarden

On Jan 23, 2013, at 10:21 PM, Li Shen wrote:

> When doing exon-centric analysis in MISO, there are always two
> isoforms related with each event. My question is: is the Psi value
> always corresponding to the "splice in" of the isoform A?
> 
> For SE event, this seems to be true. However, for other event types,
> this is not obvious. Can someone clarify?
> 
> Thanks!
> 
> --
> Li Shen, Ph.D. Computer Science
> Assistant Professor
> Department of Neuroscience
> Mount Sinai School of Medicine
> One Gustave L. Levy Place, Box 1065
> New York, NY 10029
> Phone: 212-659-8622 (office)
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