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

By Jianhua Yang, Junhao Li, Peng Shao, Hui Zhou, Yue‐Qin Chen, Liang-Hu Qu. Nucleic Acids Res., 2010

812 citations recorded by the source corpus.

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/.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/265e0782aa831558f7dff55d820e880b1366fdf1

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

1. Jianhua Yang
2. Shun Liu
3. Liang-Hu Qu
4. Junhao Li
5. Hui Zhou

In Molecular Biology

1. Jianhua Yang
2. Shun Liu
3. Liang-Hu Qu
4. Junhao Li
5. Hui Zhou

Citations in the corpus

• The bioinformatics toolbox for circRNA discovery and analysis (2020, neutral): “Many databases collect the circRNA ceRNA network such as starBase [131, 132], SomamiR [133, 134], LncACTdb [135], AFCMEasyModel [136] and HumanViCe [137].”
• ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data (2012, methodology): “miRNA targets were downloaded from starBase database (31).”
• MicroRNA dysregulation in cancer: diagnostics, monitoring and therapeutics. A comprehensive review (2012, neutral): “…these initial observations, the same group mapped all the known microRNA genes and found many of them located Review Marilena V. Iorio and Carlo M. Croce Yang et al (2011) in chromosomal loci prone to deletions or amplifications, as was found in many different human tumours (Calin et al, 2004).”
• starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data (2013, methodology): “To facilitate the annotation, visualization, analysis and discovery of these interaction networks from large-scale CLIP-Seq data, we have updated starBase (17) to version 2.0 (starBase v2.”
• RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data (2017, methodology): “To investigate whether RNA modifications influence the function of RBPs or vice versa, the relationships between CLIP-Seq experimentally supported RBP binding sites (32,33) and all RNA modification sites from RMBase were constructed.”
• miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis (2016, neutral): “(13), starBase (14) and miRecords (15).”