ArticleGenome research2002
Selecting for functional alternative splices in ESTs.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
- Power-law behavior of transcriptional bursting regulated by enhancer-promoter communication.Genome research · 2024Article
- Exon nomenclature and classification of transcripts database (ENACTdb): a resource for analyzing alternative splicing mediated proteome diversity.Bioinformatics advances · 2024Article
- 4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction.PLoS computational biology · 2023Article
- Alternative Splicing and Protein Diversity: Plants Versus Animals.Frontiers in plant science · 2019Review
- A novel RNA variant of human concentrative nucleoside transporter 1 (hCNT1) that is a potential cancer biomarker.Experimental hematology & oncology · 2019Article
- The comparison of alternative splicing among the multiple tissues in cucumber.BMC plant biology · 2018Article
- Lessons from non-canonical splicing.Nature reviews. Genetics · 2016Review
- Linking Genes to Cardiovascular Diseases: Gene Action and Gene-Environment Interactions.Journal of cardiovascular translational research · 2015Review
- Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Evolutionary Character of Alternative Splicing in Plants.Bioinformatics and biology insights · 2015Review
- Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes.Plant physiology · 2014Article
- Global dissection of alternative splicing in paleopolyploid soybean.The Plant cell · 2014Article
- The soluble form of the EIAV receptor encoded by an alternative splicing variant inhibits EIAV infection of target cells.PloS one · 2013Article
- Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidates.BMC genomics · 2012Article
- Alternative splicing: a potential source of functional innovation in the eukaryotic genome.International journal of evolutionary biology · 2012Article
- Interrogation of alternative splicing events in duplicated genes during evolution.BMC genomics · 2011Article
- Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant.Genome research · 2011Article
- The origins, evolution, and functional potential of alternative splicing in vertebrates.Molecular biology and evolution · 2011Article
- Novel RBPJ transcripts identified in human amniotic fluid cells.Stem cell reviews and reports · 2010Article
- Evolution of alternative splicing in primate brain transcriptomes.Human molecular genetics · 2010Article
28 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
The expressed sequence tag (EST) collection in dbEST provides an extensive resource for detecting alternative splicing on a genomic scale. Using genomically aligned ESTs, a computational tool (TAP) was used to identify alternative splice patterns for 6400 known human genes from the RefSeq database. With sufficient EST coverage, one or more alternatively spliced forms could be detected for nearly all genes examined. To identify high (>95%) confidence observations of alternative splicing, splice variants were clustered on the basis of having mutually exclusive structures, and sample statistics were then applied. Through this selection, alternative splices expected at a frequency of >5% within their respective clusters were seen for only 17%-28% of genes. Although intron retention events (potentially unspliced messages) had been seen for 36% of the genes overall, the same statistical selection yielded reliable cases of intron retention for <5% of genes. For high-confidence alternative splices in the human ESTs, we also noted significantly higher rates both of cross-species conservation in mouse ESTs and of validation in the GenBank mRNA collection. We suggest quantitative analytical approaches such as these can aid in selecting useful targets for further experimental characterization and in so doing may help elucidate the mechanisms and biological implications of alternative splicing.
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