ArticleRNA (New York, N.Y.)2015
Leveraging transcript quantification for fast computation of alternative splicing profiles.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
161 citing papers in PubMed.
- CB1 receptor inhibition restores synaptoneurosomal alternative splicing landscape in fragile X syndrome mice.iScience · 2026Article
- Alternative splicing dynamics in pig tissues under soybean oil supplementation.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Chromosome level genome assembly and full-length transcriptome of blacktip trevally (Caranx heberi).Scientific data · 2026Article
- Splicing Factor SR45 Enhances Cold Tolerance in Cassava by Recruiting Nu4A Complex and Transcription Factors to Activate WRKY30.Plant, cell & environment · 2026Article
- IRCAS: a novel end-to-end approach to identify, rectify, and classify comprehensive alternative splicing events in a transcriptome without genome reference.Briefings in bioinformatics · 2026Article
- Phased T2T genome of a tetraploid grapevine reveals segmental allopolyploid origin and allele-specific alternative splicing during fruit development.Plant physiology · 2026Article
- Multi-omic screening identifies RBMXL3 as a primate-specific RNA-binding protein and candidate regulator of RNA metabolism in human spermatogenesis.Cellular & molecular biology letters · 2026Article
- The RNA helicase DDX53 (CAGE) contributes to RNA metabolism in a human germ cell model.bioRxiv : the preprint server for biology · 2026Article
- Identification and Characterization of sQTLs and eQTLs Associated with Growth Traits in Yellow-Feathered Broilers.Poultry science · 2026Article
- Chromosome level genome and full length transcriptome of long whiskers catfish, Mystus gulio (Hamilton, 1822).Scientific data · 2026Article
- Machine learning framework for mRNA alternative splicing analysis identifies a signature of progression in colorectal adenocarcinoma.Scientific reports · 2026Article
- Transcript isoforms and alternative splicing in polyploid Brassica napus under heat and cold stress.Annals of botany · 2026Article
- ACmix-Swin Deep Learning of 4-Day-OldGenes · 2025Article
- piRNAs safeguard splicing and RNA fidelity during heat shock.bioRxiv : the preprint server for biology · 2025Article
- Integrating WGCNA, TCN, and Alternative Splicing to Map Early Caste Programs in Day-2 Honeybee Larvae.Genes · 2025Article
- The implications of alternative splicing regulation for maximum lifespan.Nature communications · 2025Article
- Phosphorus starvation-induced alternative splicing landscape of rice confirms the regulatory function of Pup1 QTL.BMC plant biology · 2025Article
- Deciphering splicing heterogeneity at single-cell resolution by SCSES.Nature communications · 2025Article
- The Implications of Alternative Splicing Regulation for Maximum Lifespan.bioRxiv : the preprint server for biology · 2025Article
- Full-Length Transcriptome Analysis of Alternative Splicing and Polyadenylation in the Molecular Regulation of Labor Division inInternational journal of molecular sciences · 2025Article
101 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing plays an essential role in many cellular processes and bears major relevance in the understanding of multiple diseases, including cancer. High-throughput RNA sequencing allows genome-wide analyses of splicing across multiple conditions. However, the increasing number of available data sets represents a major challenge in terms of computation time and storage requirements. We describe SUPPA, a computational tool to calculate relative inclusion values of alternative splicing events, exploiting fast transcript quantification. SUPPA accuracy is comparable and sometimes superior to standard methods using simulated as well as real RNA-sequencing data compared with experimentally validated events. We assess the variability in terms of the choice of annotation and provide evidence that using complete transcripts rather than more transcripts per gene provides better estimates. Moreover, SUPPA coupled with de novo transcript reconstruction methods does not achieve accuracies as high as using quantification of known transcripts, but remains comparable to existing methods. Finally, we show that SUPPA is more than 1000 times faster than standard methods. Coupled with fast transcript quantification, SUPPA provides inclusion values at a much higher speed than existing methods without compromising accuracy, thereby facilitating the systematic splicing analysis of large data sets with limited computational resources. The software is implemented in Python 2.7 and is available under the MIT license at https://bitbucket.org/regulatorygenomicsupf/suppa.
Indexed as
Identifiers
What OpenQuestion holds
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.