ArticleGenome biology2011
Coding potential of the products of alternative splicing in human.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- CaTCH: Calculating transcript complexity of human genes.MethodsX · 2024Article
- RNA-Based Strategies for Cancer Therapy: In Silico Design and Evaluation of ASOs for Targeted Exon Skipping.International journal of molecular sciences · 2023Article
- Long noncoding RNA LINC01594 inhibits the CELF6-mediated splicing of oncogenic CD44 variants to promote colorectal cancer metastasis.Cell death & disease · 2023Article
- Re-evaluating the impact of alternative RNA splicing on proteomic diversity.Frontiers in genetics · 2023Review
- Integration of TE Induces Cancer Specific Alternative Splicing Events.International journal of molecular sciences · 2022Review
- The ChloroplastCells · 2021Review
- AI applications in functional genomics.Computational and structural biotechnology journal · 2021Review
- Correlations Between the Characteristics of Alternative Splicing Events, Prognosis, and the Immune Microenvironment in Breast Cancer.Frontiers in genetics · 2021Article
- Enteric infection induces Lark-mediated intron retention at the 5' end of Drosophila genes.Genome biology · 2020Article
- The biological function and clinical significance of SF3B1 mutations in cancer.Biomarker research · 2020Review
- Identification of Prognostic Alternative Splicing Signature in Breast Carcinoma.Frontiers in genetics · 2019Article
- Extensive Alternative Splicing of KIR Transcripts.Frontiers in immunology · 2018Article
- Impact of Alternative Splicing on the Human Proteome.Cell reports · 2017Article
- Chemosensory adaptations of the mountain fly Drosophila nigrosparsa (Insecta: Diptera) through genomics' and structural biology's lenses.Scientific reports · 2017Article
- Alternative splicing and the evolution of phenotypic novelty.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- Proteogenomics: concepts, applications and computational strategies.Nature methods · 2014Review
- Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity.Molecular biology and evolution · 2014Article
- Misregulation of pre-mRNA alternative splicing in cancer.Cancer discovery · 2013Review
- Differential splicing across immune system lineages.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq.Molecular & cellular proteomics : MCP · 2013Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAnalysis of the human genome has revealed that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized genes. A number of these transcripts are alternatively spliced forms of known protein coding genes; however, it is becoming clear that many of them do not necessarily correspond to a functional protein.
resultsIn this study we analyze alternative splicing isoforms of human gene products that are unambiguously identified by mass spectrometry and compare their properties with those of isoforms of the same genes for which no peptide was found in publicly available mass spectrometry datasets. We analyze them in detail for the presence of uninterrupted functional domains, active sites as well as the plausibility of their predicted structure. We report how well each of these strategies and their combination can correctly identify translated isoforms and derive a lower limit for their specificity, that is, their ability to correctly identify non-translated products.
conclusionsThe most effective strategy for correctly identifying translated products relies on the conservation of active sites, but it can only be applied to a small fraction of isoforms, while a reasonably high coverage, sensitivity and specificity can be achieved by analyzing the presence of non-truncated functional domains. Combining the latter with an assessment of the plausibility of the modeled structure of the isoform increases both coverage and specificity with a moderate cost in terms of sensitivity.
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