ArticleNucleic acids research2010
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed.
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- A reliable and quick method for screening alternative splicing variants for low-abundance genes.PloS one · 2024Article
- TiSA: TimeSeriesAnalysis-a pipeline for the analysis of longitudinal transcriptomics data.NAR genomics and bioinformatics · 2023Article
- Towards a Systems Immunology Approach to Understanding Correlates of Protective Immunity against HCV.Viruses · 2021Review
- Alternatively Splicing Interactomes Identify Novel Isoform-Specific Partners for NSD2.Frontiers in cell and developmental biology · 2021Article
- Intrinsically disordered protein RBM14 plays a role in generation of RNA:DNA hybrids at double-strand break sites.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Transcriptomic Analysis of Testicular Gene Expression in Normal and Cryptorchid Horses.Animals : an open access journal from MDPI · 2020Article
- Optimization of Insect Odorant Receptor Trafficking and Functional Expression Via Transient Transfection in HEK293 Cells.Chemical senses · 2019Article
- Temporal dynamics in meta longitudinal RNA-Seq data.Scientific reports · 2019Article
- Gene co-expression analysis for functional classification and gene-disease predictions.Briefings in bioinformatics · 2018Article
- Isoform-level gene expression patterns in single-cell RNA-sequencing data.Bioinformatics (Oxford, England) · 2018Article
- Paradigm for disease deconvolution in rare neurodegenerative disorders in Indian population: insights from studies in cerebellar ataxias.Journal of genetics · 2018Article
- Delineating inflammatory bowel disease through transcriptomic studies: current review of progress and evidence.Intestinal research · 2018Review
- Exon Array Biomarkers for the Differential Diagnosis of Schizophrenia and Bipolar Disorder.Molecular neuropsychiatry · 2018Article
- Whole Transcriptome Profiling: An RNA-Seq Primer and Implications for Pharmacogenomics Research.Clinical and translational science · 2018Review
- Cytochrome P450 family proteins as potential biomarkers for ovarian granulosa cell damage in mice with premature ovarian failure.International journal of clinical and experimental pathology · 2018Article
- Analysis and Prediction of Exon Skipping Events from RNA-Seq with Sequence Information Using Rotation Forest.International journal of molecular sciences · 2017Article
- Structural basis for spumavirus GAG tethering to chromatin.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Androgen receptor-deficient islet β-cells exhibit alteration in genetic markers of insulin secretion and inflammation. A transcriptome analysis in the male mouse.Journal of diabetes and its complications · 2017Article
- Clustering of mRNA-Seq data based on alternative splicing patterns.Biostatistics (Oxford, England) · 2017Article
25 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing, polyadenylation of pre-messenger RNA molecules and differential promoter usage can produce a variety of transcript isoforms whose respective expression levels are regulated in time and space, thus contributing specific biological functions. However, the repertoire of mammalian alternative transcripts and their regulation are still poorly understood. Second-generation sequencing is now opening unprecedented routes to address the analysis of entire transcriptomes. Here, we developed methods that allow the prediction and quantification of alternative isoforms derived solely from exon expression levels in RNA-Seq data. These are based on an explicit statistical model and enable the prediction of alternative isoforms within or between conditions using any known gene annotation, as well as the relative quantification of known transcript structures. Applying these methods to a human RNA-Seq dataset, we validated a significant fraction of the predictions by RT-PCR. Data further showed that these predictions correlated well with information originating from junction reads. A direct comparison with exon arrays indicated improved performances of RNA-Seq over microarrays in the prediction of skipped exons. Altogether, the set of methods presented here comprehensively addresses multiple aspects of alternative isoform analysis. The software is available as an open-source R-package called Solas at http://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/.
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