ASpedia: a comprehensive encyclopedia of human alternative splicingopen access
- Authors
- Hyung, Daejin; Kim, Jihyun; Cho, Soo Young; Park, Charny
- Issue Date
- Jan-2018
- Publisher
- Oxford University Press
- Citation
- Nucleic Acids Research, v.46, no.D1, pp D58 - D63
- Indexed
- SCI
SCIE
SCOPUS
- Journal Title
- Nucleic Acids Research
- Volume
- 46
- Number
- D1
- Start Page
- D58
- End Page
- D63
- URI
- https://scholarworks.bwise.kr/erica/handle/2021.sw.erica/114376
- DOI
- 10.1093/nar/gkx1014
- ISSN
- 0305-1048
1362-4962
- Abstract
- Alternative splicing confers the human genome complexity by increasing the diversity of expressed mRNAs. Hundreds or thousands of splicing regions have been identified through differential alternative splicing analysis of high-throughput datasets. However, it is hard to explain the functional impact of each splicing event. Protein domain formation and nonsense-mediated decay are considered the main functional features of splicing. However, other functional features such as miRNA target sites, phosphorylation sites and single-nucleotide variations are directly affected by alternative splicing and affect downstream function. Hence, we established ASpedia: A comprehensive database for human alternative splicing annotation, which encompasses a range of functions, from genomic annotation to isoform-specific function (ASpedia, http://combio.snu.ac.kr/aspedia). The database provides three features: (i) genomic annotation extracted from DNA, RNA and proteins; (ii) transcription and regulation elements analyzed from next-generation sequencing datasets; and (iii) isoform-specific functions collected from known and published datasets. The ASpedia web application includes three components: An annotation database, a retrieval system and a browser specialized in the identification of human alternative splicing events. The retrieval system supports multiple AS event searches resulting from high-throughput analysis and the AS browser comprises genome tracks. Thus, ASpedia facilitates the systemic annotation of the functional impacts of multiple AS events. © 2017 The Author(s).
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