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ASpedia: a comprehensive encyclopedia of human alternative splicing.
Daejin Hyung1,2, Jihyun Kim1, Soo Young Cho1
1Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang-si, Kyeonggi-do 10408, Republic of Korea.
Nucleic Acids Research
|November 7, 2017
Summary
ASpedia is a new database that provides comprehensive human alternative splicing annotation. It links genomic data to isoform-specific functions, aiding in understanding splicing event impacts.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Alternative splicing significantly increases human genome complexity and mRNA diversity.
- Understanding the functional impact of individual splicing events remains a challenge.
- Beyond protein domains and nonsense-mediated decay, splicing affects miRNA targets, phosphorylation sites, and SNPs.
Purpose of the Study:
- To establish ASpedia, a comprehensive database for human alternative splicing annotation.
- To integrate genomic annotation with isoform-specific functions.
- To facilitate the systemic annotation of alternative splicing event impacts.
Main Methods:
- ASpedia integrates genomic annotation from DNA, RNA, and protein data.
- It analyzes transcription and regulatory elements from next-generation sequencing datasets.
- Isoform-specific functions are collected from existing and published datasets.
Main Results:
- ASpedia provides genomic annotation, transcription/regulation analysis, and isoform-specific functions.
- The database features an annotation database, a retrieval system, and a specialized browser.
- The retrieval system supports searches for multiple alternative splicing events.
Conclusions:
- ASpedia offers a valuable resource for understanding human alternative splicing.
- It facilitates the annotation of functional impacts across multiple splicing events.
- The database aids in exploring the link between alternative splicing and downstream cellular functions.