starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

• Published in: Nucleic acids research Vol. 39; no. suppl_1; pp. D202 - D209
• Main Authors: Yang, Jian-Hua, Li, Jun-Hao, Shao, Peng, Zhou, Hui, Chen, Yue-Qin, Qu, Liang-Hu
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2011
• Subjects: Animals; Binding Sites; Databases, Nucleic Acid; Gene Expression Regulation; Genomics; Humans; Internet; Mice; MicroRNAs - chemistry; MicroRNAs - metabolism; RNA, Messenger - chemistry; RNA, Messenger - metabolism; RNA-Binding Proteins - metabolism; Sequence Analysis, RNA; Software; User-Computer Interface
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkq1056

MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (sRNAs) that regulate gene expression by targeting messenger RNAs. However, assigning miRNAs to their regulatory target genes remains technically challenging. Recently, high-throughput CLIP-Seq and degradome sequencing (Degradome-Seq) methods have been applied to identify the sites of Argonaute interaction and miRNA cleavage sites, respectively. In this study, we introduce a novel database, starBase (sRNA target Base), which we have developed to facilitate the comprehensive exploration of miRNA-target interaction maps from CLIP-Seq and Degradome-Seq data. The current version includes high-throughput sequencing data generated from 21 CLIP-Seq and 10 Degradome-Seq experiments from six organisms. By analyzing millions of mapped CLIP-Seq and Degradome-Seq reads, we identified ~1 million Ago-binding clusters and ~2 million cleaved target clusters in animals and plants, respectively. Analyses of these clusters, and of target sites predicted by 6 miRNA target prediction programs, resulted in our identification of approximately 400 000 and approximately 66 000 miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively. Furthermore, two web servers were provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. Our web implementation supports diverse query types and exploration of common targets, gene ontologies and pathways. The starBase is available at http://starbase.sysu.edu.cn/.