splicing analysis of Exon ST arrays

[Andrea Cortese]

Dear members of the staff,
We have performed Exon ST arrays (Affymetrix) on muscle tisse of 2
different myopathies and normal muscle tissue (13 samples overall). Beside
gene expression differences, we would be interested also in picking up
possible splicing alterations. Do you think it is still possible to get
good results if we analyze those platforms through altanalyze (I noticed
the tutorial and manual are basically targeted to exon junction and RNAseq
regarding splicing analysis, and I am aweare that Ex junction and RNA seq
are more sensible to alernative splicing detection)?
Thanks for your help
Andrea

[Nathan Salomonis]

Hi Andrea,

Actually, AltAnalyze was first described for use of Exon arrays and 90% or more of publications for AltAnalyze have been for exon arrays, see:
http://code.google.com/p/altanalyze/wiki/CitingArticles

A good overview of what AltAnalyze can do for exon arrays can be found here:
http://nar.oxfordjournals.org/content/early/2010/05/31/nar.gkq405.full

Basically, yes, I find good agreement between exon array, junction array and RNA-Seq analyses, depending on the quality of the input data. I have found as much as 90% of predicted alternative exons can be validated by RT-PCR (e.g., reactions flanking the regulated exon). Let me know if you have questions regarding your specific results.

Best,
Nathan

Andrea

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