Aternative splicing

Donogh O'Brien

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Jun 24, 2016, 11:00:38 AM6/24/16

to UCSC Xena and Cancer Genomics Browser

Hi
I'm interested in finding out what the relative abundance is of two transcripts produced by alternative splicing of two 3' exons (gene MKNK2). In the TCGA BRCA RNAseq exon seq heat map both these exons map to the same probeset so I can't distinguish between the transcripts. Is there some way I can get this information? I guess in this instance "probeset" refers to a collection of neighboring reads?
Thanks for your help
best regards
Don

Mary Goldman

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Jun 24, 2016, 11:20:18 AM6/24/16

to Donogh O'Brien, UCSC Xena and Cancer Genomics Browser

Hi Don,

I would actually recommend using Xena and the GA4GH/BD2K TOIL recompute of the TCGA data which has transcript specific expression.

Obtain the Ensembl IDs of the transcripts you are interested in and go to our visualization. Choose 'TCGA Pan-Cancer (PANCAN)'. Next choose 'transcript expression RNAseq' at the bottom of the list. Finally click on 'identifiers' and enter your Ensembl IDs.

You can limit your view to just BRCA by using the 'Samples in' filter and selecting 'breast invasive carcinoma'

Right now some of the IDs we have mapped to MKN2 are: ENST00000589441.5 ENST00000591142.5 ENST00000591601.5 ENST00000309340.11 ENST00000587416.5 ENST00000250896.7 ENST00000588014.5 ENST00000586828.5 ENST00000591588.1 ENST00000585667.1 ENST00000586620.2 ENST00000589509.5 ENST00000589534.2

Do you see yours in there?

Best,
Mary
-------------
Mary Goldman
UCSC Xena Browser
http://xena.ucsc.edu/

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Donogh O'Brien

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Jun 30, 2016, 12:20:28 PM6/30/16

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Thanks Mary- my transcripts are all there.

Mary Goldman

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Jun 30, 2016, 12:22:48 PM6/30/16

to Donogh O'Brien, UCSC Xena and Cancer Genomics Browser

Hi Don,

Oh good! As always, email us with any of your questions or comments.

Best,
Mary
-------------
Mary Goldman
UCSC Xena Browser
http://xena.ucsc.edu/

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Donogh O'Brien

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Aug 1, 2016, 1:45:22 PM8/1/16

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Hi Mary

I did what you suggested and found the transcript percentages I was looking for. I would like to know more about how TOIL derives these percentages- is it based on reads across specific splice sites? Perhaps there is some documentation you can recommend. I think this is a really useful addition to Xena which opens up all sorts of new possibilities. I was looking at SRSF1 which has isoforms which accelerate or repress splicing and if I can reliably determine percentages of each isoform in a cancer setting this could be very informative.

Many thanks

Best regards

Don

Le vendredi 24 juin 2016 17:00:38 UTC+2, Donogh O'Brien a écrit :

Jing Zhu

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Aug 1, 2016, 4:52:24 PM8/1/16

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Hi Don,

The transcript percentages data comes from RSEM method. It is part of the standard RSEM output. RSEM analysis is part of the TOIL (UCSC BD2K developed) RNAseq analysis pipeline,

For more information about the TOIL pipeline, see

http://dx.doi.org/10.1101/062497

http://xena.ucsc.edu/public-hubs/

Please cite http://dx.doi.org/10.1101/062497 and http://xena.ucsc.edu when using of the datasest. Thanks.

Jing

Mary Goldman

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Aug 1, 2016, 5:00:42 PM8/1/16

to Jing Zhu, UCSC Xena and Cancer Genomics Browser

Hi Don,

This link may also be helpful: https://genome-cancer.soe.ucsc.edu/proj/site/xena/datapages/?host=https://toil.xenahubs.net