Journal
BIOINFORMATICS
Volume 25, Issue 23, Pages 3056-3059Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btp544
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Funding
- National Institute of Health [R01-HG004634, U54-GM062119]
- Ric Weiland Graduate Fellowship
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Motivation: Splice junction microarrays and RNA-seq are two popular ways of quantifying splice variants within a cell. Unfortunately, isoform expressions cannot always be determined from the expressions of individual exons and splice junctions. While this issue has been noted before, the extent of the problem on various platforms has not yet been explored, nor have potential remedies been presented. Results: We propose criteria that will guarantee identifiability of an isoform deconvolution model on exon and splice junction arrays and in RNA-Seq. We show that up to 97% of 2256 alternatively spliced human genes selected from the RefSeq database lead to identifiable gene models in RNA-seq, with similar results in mouse. However, in the Human Exon array only 26% of these genes lead to identifiable models, and even in the most comprehensive splice junction array only 69% lead to identifiable models.
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