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

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 DegradomeSeq 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...

• Type: Journal
• Year: 2011
• Where: NAR
• Authors: Jian-Hua Yang, Jun-Hao Li, Peng Shao, Hui Zhou, Yue-Qin Chen, Liang-Hu Qu
• Keywords: NAR 2011, Regulatory Relationships, Target Genes, Web Implementation