ArticlePloS one2016
Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 30 citations in OpenAlex.
- mRNA Isoforms and Variants in Health and Disease.International journal of molecular sciences · 2025Review
- mRNA Transcript Variants Expressed in Mammalian Cells.International journal of molecular sciences · 2025Review
- Identification and validation of biomarkers related to nicotinamide metabolic pathway activity in heart failure.Frontiers in genetics · 2025Article
- Transcriptomic Alterations in Spliceosome Components in Advanced Heart Failure: Status of Cardiac-Specific Alternative Splicing Factors.International journal of molecular sciences · 2024Article
- Alternative splicing of modulatory immune receptors in T lymphocytes: a newly identified and targetable mechanism for anticancer immunotherapy.Frontiers in immunology · 2024Review
- The identification of protein and RNA interactors of the splicing factor Caper in the adultFrontiers in molecular neuroscience · 2023Article
- Article
- Transcript isoforms of Reep6 have distinct functions in the retina.Human molecular genetics · 2021Article
- MTSplice predicts effects of genetic variants on tissue-specific splicing.Genome biology · 2021Article
- Creation and validation of models to predict response to primary treatment in serous ovarian cancer.Scientific reports · 2021Article
- Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes.International journal of molecular sciences · 2019Review
- The LL-100 panel: 100 cell lines for blood cancer studies.Scientific reports · 2019Article
- Pathogenicity and selective constraint on variation near splice sites.Genome research · 2019Article
- Combinatorial Pattern of Histone Modifications in Exon Skipping Event.Frontiers in genetics · 2019Article
- Microcephaly Modeling of Kinetochore Mutation Reveals a Brain-Specific Phenotype.Cell reports · 2018Article
- Transcriptional Profiling of Host Cell Responses to VirulentInternational journal of molecular sciences · 2018Article
- The determinants of alternative RNA splicing in human cells.Molecular genetics and genomics : MGG · 2017Review
- Computer Analysis of Glioma Transcriptome Profiling: Alternative Splicing Events.Journal of integrative bioinformatics · 2017Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing is a vital process for regulating gene expression and promoting proteomic diversity. It plays a key role in tissue-specific expressed genes. This specificity is mainly regulated by splicing factors that bind to specific sequences called splicing regulatory elements (SREs). Here, we report a genome-wide analysis to study alternative splicing on multiple tissues, including brain, heart, liver, and muscle. We propose a pipeline to identify differential exons across tissues and hence tissue-specific SREs. In our pipeline, we utilize the DEXSeq package along with our previously reported algorithms. Utilizing the publicly available RNA-Seq data set from the Human BodyMap project, we identified 28,100 differentially used exons across the four tissues. We identified tissue-specific exonic splicing enhancers that overlap with various previously published experimental and computational databases. A complicated exonic enhancer regulatory network was revealed, where multiple exonic enhancers were found across multiple tissues while some were found only in specific tissues. Putative combinatorial exonic enhancers and silencers were discovered as well, which may be responsible for exon inclusion or exclusion across tissues. Some of the exonic enhancers are found to be co-occurring with multiple exonic silencers and vice versa, which demonstrates a complicated relationship between tissue-specific exonic enhancers and silencers.
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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.