AS event column is empty (no annotation of cassette exon/alt-N-term/alt-C-term) in DomainGraph

[Adol]

Hi everyone!

I wonder if someone worked with AltAnalyze output in DomainGraph/Cytoscape and faced the same problem: the AS (alternative event column is empty (not a single exon is annotated as e.g. alt-N-term, alt-C-term or cassette-exon [I need to sort the list, based on this annotation]. I performed the instaIlation of Cytoscape 2.8.3 and then DomainGraph PlugIn (release 3.0)  and downloaded the ENS_52 library for Homo sapiens. Then I started the DomainGraph and uploaded the AltAnalyze .txt file with results of alternative splicing from folder DomainGraph. I wonder, if I missed something and did not installed the right library. 

Thank you very much for your help and input,

Best Regards,

Anna

[Nathan Salomonis]

Hi Anna,

I believe this is what you see with the latest DomainGraph database version (missing alt exon annotations), which is an annotation issue with that database (version 65). But if you download the EnsMart54 or 55 database, those annotations should be present. This is something we have hoped to address in the next database build which is taking a bit longer than normal as we have been waiting for Affymetrix to update it's mouse genome reference to mm10.

Best,
Nathan

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