Question: How to get expression data about mutually exclusive exons from TCGA or GDC
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gravatar for fk506
12 months ago by
fk5060
fk5060 wrote:

Hi everyone.

I'm a beginner of analysis about splicing variants.

I'm now interested in what mutually exclusive exons in some genes express dominantly in some cancers.
I want to know how to get expression data about mutually exclusive exons from TCGA or GDC.

In annotation file, I confirmed that there are 775373 of "componentExon"s and there are 276914 of unique "FeatureID"s.
https://gdc.cancer.gov/download-gdc-reference-files
TCGA.hg19.June2011.gaf (md5: b9e0c2b81736d82d62bb6ab8cc517644)

However, exon quantification data from GDC or TCGA RNA-seqV2 contains only 239322 of Hybridization.REF and 60492 "FeatureID"s are not contained in the data.
FeatureInfo about FeatureIDs which are not contained in exon quantification data are such as "ExonName=exon9J_WASH7P|653635", "ExonName=exon18B_KIAA1274|27143"...they suggest these exons are mutually exclusive exons.

It seems to be many of mutually exclusive exons are not included in "exon quantification data".
Anyone know why these exons are not included in TCGA exon quantification data?
Anyone know where expression data about these exons is deposited?

Thanks

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