TY - JOUR
AU - Qu, Liang-Hu
AB - 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 miRNAtarget 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 400000 and approximately 66000 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/.
TI - starBase: a database for exploring microRNAmRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data
JF - Nucleic Acids Research
DO - 10.1093/nar/gkq1056
DA - 2011-01-30
UR - https://www.deepdyve.com/lp/oxford-university-press/starbase-a-database-for-exploring-micrornamrna-interaction-maps-from-A65NmPnFtS
SP - D202
EP - D209
VL - 39
IS - suppl_1
DP - DeepDyve
ER -