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Nucleic Acids Res. 2018 Jan 4;46(D1):D58-D63. doi: 10.1093/nar/gkx1014.

ASpedia: a comprehensive encyclopedia of human alternative splicing.

Author information

1
Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang-si, Kyeonggi-do 10408, Republic of Korea.
2
Department of Computer Engineering, Dong-A University, 37 Nakdong-daero 550 Beon-gil, Saha-gu, Busan 49315, Republic of Korea.

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.

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