ArticleBMC genomics2012
Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- Review
- Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.World journal of stem cells · 2021Review
- Prp8 impacts cryptic but not alternative splicing frequency.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- SNRP-27, theRNA (New York, N.Y.) · 2018Article
- Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data.Current genomics · 2017Review
- Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages.PLoS genetics · 2016Article
- Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data.BMC genomics · 2016Article
- ISOexpresso: a web-based platform for isoform-level expression analysis in human cancer.BMC genomics · 2016Article
- Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics.Scientific reports · 2015Article
- A survey of computational methods in transcriptome-wide alternative splicing analysis.Biomolecular concepts · 2015Review
- spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.BMC bioinformatics · 2014Article
- Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data.PloS one · 2014Article
- Genomics in 2012: challenges and opportunities in the next generation sequencing era.BMC genomics · 2012Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundAlternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splicing.
resultsWe developed Alt Event Finder, a tool for identifying novel splicing events by using transcript annotation derived from genome-guided construction tools, such as Cufflinks and Scripture. With a proper combination of alignment and transcript reconstruction tools, Alt Event Finder is capable of identifying novel splicing events in the human genome. We further applied Alt Event Finder on a set of RNA-seq data from rat liver tissues, and identified dozens of novel cassette exon events whose splicing patterns changed after extensive alcohol exposure.
conclusionsAlt Event Finder is capable of identifying de novo splicing events from data-driven transcript annotation, and is a useful tool for studying splicing regulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.