ArticleBioinformatics (Oxford, England)2009
Identifiability of isoform deconvolution from junction arrays and RNA-Seq.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Selecting differential splicing methods: Practical considerations for short-read RNA sequencing.F1000Research · 2025Review
- Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Pervasive 3'-UTR Isoform Switches During Mouse Oocyte Maturation.Frontiers in molecular biosciences · 2021Article
- A computational system for identifying operons based on RNA-seq data.Methods (San Diego, Calif.) · 2020Review
- High resolution annotation of zebrafish transcriptome using long-read sequencing.Genome research · 2018Article
- Bayesian nonparametric discovery of isoforms and individual specific quantification.Nature communications · 2018Article
- Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms.Briefings in bioinformatics · 2017Article
- RNA-Seq Data: A Complexity Journey.Computational and structural biotechnology journal · 2014Review
- Next generation sequencing in cardiomyopathy: towards personalized genomics and medicine.Molecular biology reports · 2014Review
- Computational approaches for isoform detection and estimation: good and bad news.BMC bioinformatics · 2014Article
- The impacts of read length and transcriptome complexity for de novo assembly: a simulation study.PloS one · 2014Article
- Characterization of the human ESC transcriptome by hybrid sequencing.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.Bioinformatics (Oxford, England) · 2013Article
- Simultaneous isoform discovery and quantification from RNA-seq.Statistics in biosciences · 2013Article
- Accurate detection of differential RNA processing.Nucleic acids research · 2013Article
- Article
- Potential roles of microRNAs in regulating long intergenic noncoding RNAs.BMC medical genomics · 2013Article
- Differential analysis of gene regulation at transcript resolution with RNA-seq.Nature biotechnology · 2013Article
- Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research.PloS one · 2012Article
- IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.BMC bioinformatics · 2011Article
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Authors and funding
4 authors.
Funding
Abstract
motivationSplice 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.
resultsWe 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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