ArticleGenome research2017
Identification of protein features encoded by alternative exons using Exon Ontology.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 68 citations in OpenAlex.
- Review
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- hnRNPU Safeguards Oocyte Development and Female Fertility via Regulation of Alternative Splicing.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Dysregulated RNA splicing impairs regeneration in alcohol-associated liver disease.Nature communications · 2025Article
- Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity.Genome research · 2025Article
- ESRP2-microRNA-122 axis promotes the postnatal onset of liver polyploidization and maturation.Genes & development · 2025Article
- Toward a comprehensive profiling of alternative splicing proteoform structures, interactions and functions.Current opinion in structural biology · 2025Review
- Deciphering a profiling based on multiple post-translational modifications functionally associated regulatory patterns and therapeutic opportunities in human hepatocellular carcinoma.Molecular cancer · 2024Article
- PTBP1 mediates Sertoli cell actin cytoskeleton organization by regulating alternative splicing of actin regulators.Nucleic acids research · 2024Article
- junctionCounts: comprehensive alternative splicing analysis and prediction of isoform-level impacts to the coding sequence.NAR genomics and bioinformatics · 2024Article
- PTBP1 mediates Sertoli cell actin cytoskeleton organization by regulating alternative splicing of actin regulators.bioRxiv : the preprint server for biology · 2024Article
- Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity.bioRxiv : the preprint server for biology · 2024Article
- An alternative splicing signature defines the basal-like phenotype and predicts worse clinical outcome in pancreatic cancer.Cell reports. Medicine · 2024Article
- SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors.Database : the journal of biological databases and curation · 2023Article
- PTBP1 controls intestinal epithelial regeneration through post-transcriptional regulation of gene expression.Nucleic acids research · 2023Article
- Advances in epigenetic modifications of autophagic process in pulmonary hypertension.Frontiers in immunology · 2023Review
- Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease.Human molecular genetics · 2022Review
- Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic β cells.Science advances · 2022Article
Corrections and comments
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Authors and funding
16 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named "Exon Ontology," based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information.
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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.