ArticleNucleic acids research2010
Computational identification of tissue-specific alternative splicing elements in mouse genes from RNA-Seq.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Splicing defects and CRISPR-Cas9 correction in isogenic homozygous photoreceptor precursors harboring clustered deep-intronic ABCA4 variants.Molecular therapy. Nucleic acids · 2024Article
- TDP43 promotes stemness of breast cancer stem cells through CD44 variant splicing isoforms.Cell death & disease · 2022Article
- Transcript isoforms of Reep6 have distinct functions in the retina.Human molecular genetics · 2021Article
- Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data.PloS one · 2016Article
- CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements.BMC bioinformatics · 2015Article
- Genome-wide analysis of alternative transcripts in human breast cancer.Breast cancer research and treatment · 2015Article
- Identifying splicing regulatory elements with de Bruijn graphs.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- A biophysical model for identifying splicing regulatory elements and their interactions.PloS one · 2013Article
- VERSE: a varying effect regression for splicing elements discovery.Journal of computational biology : a journal of computational molecular cell biology · 2012Article
- Genetic variations and alternative splicing: the Glioma associated oncogene 1, GLI1.Frontiers in genetics · 2012Article
- Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.BMC genomics · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tissue-specific alternative splicing is a key mechanism for generating tissue-specific proteomic diversity in eukaryotes. Splicing regulatory elements (SREs) in pre-mature messenger RNA play a very important role in regulating alternative splicing. In this article, we use mouse RNA-Seq data to determine a positive data set where SREs are over-represented and a reliable negative data set where the same SREs are most likely under-represented for a specific tissue and then employ a powerful discriminative approach to identify SREs. We identified 456 putative splicing enhancers or silencers, of which 221 were predicted to be tissue-specific. Most of our tissue-specific SREs are likely different from constitutive SREs, since only 18% of our exonic splicing enhancers (ESEs) are contained in constitutive RESCUE-ESEs. A relatively small portion (20%) of our SREs is included in tissue-specific SREs in human identified in two recent studies. In the analysis of position distribution of SREs, we found that a dozen of SREs were biased to a specific region. We also identified two very interesting SREs that can function as an enhancer in one tissue but a silencer in another tissue from the same intronic region. These findings provide insight into the mechanism of tissue-specific alternative splicing and give a set of valuable putative SREs for further experimental investigations.
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