ArticleF1000Research2013
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues.
Article in F1000Research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 314 papers.
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Who cites it
314 citing papers in PubMed, 439 citations in OpenAlex.
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- Benchmarking foundation models for splice site and exon annotation.bioRxiv : the preprint server for biology · 2026Article
- Static Magnetic Field Promotes Wheat Nitrogen Assimilation by Repressing Jasmonates Biosynthesis Through TaHY5.Plant biotechnology journal · 2026Article
- De novo variants in the splicing factor gene SF3B1 are associated with neurodevelopmental disorders.Nature communications · 2026Article
- A Comparative Analysis of Transcriptome-Wide Differential Gene Expression and Alternative Polyadenylation in the Ovaries of Meat Ducks and Laying Ducks.Animals : an open access journal from MDPI · 2026Article
- Genomic basis underlying alternative transcripts-mediated drought tolerance in maize.Genome biology · 2026Article
- Cold adaptation mechanism in Bactrocera dorsalis (Diptera: Tephritidae) by regulating MAPK signaling and metabolic pathways.Journal of insect science (Online) · 2026Article
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- Transcriptomic Profiling of mRNA and lncRNA During the Developmental Transition from Spores to Mycelia inMicroorganisms · 2025Article
254 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. However, despite many efforts, the repertoire of gene splicing variation is still incompletely characterized, even in humans. Here we describe a new computational system, ASprofile, and its application to RNA-seq data from Illumina's Human Body Map project (>2.5 billion reads). Using the system, we identified putative alternative splicing events in 16 different human tissues, which provide a dynamic picture of splicing variation across the tissues. We detected 26,989 potential exon skipping events representing differences in splicing patterns among the tissues. A large proportion of the events (>60%) were novel, involving new exons (~3000), new introns (~16000), or both. When tracing these events across the sixteen tissues, only a small number (4-7%) appeared to be differentially expressed ('switched') between two tissues, while 30-45% showed little variation, and the remaining 50-65% were not present in one or both tissues compared. Novel exon skipping events appeared to be slightly less variable than known events, but were more tissue-specific. Our study represents the first effort to build a comprehensive catalog of alternative splicing in normal human tissues from RNA-seq data, while providing insights into the role of alternative splicing in shaping tissue transcriptome differences. The catalog of events and the ASprofile software are freely available from the Zenodo repository ( http://zenodo.org/record/7068; doi: 10.5281/zenodo.7068) and from our web site http://ccb.jhu.edu/software/ASprofile.
Identifiers
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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.