| Chapter title |
Discovery of microRNA Regulatory Networks by Integrating Multidimensional High-Throughput Data.
|
|---|---|
| Chapter number | 13 |
| Book title |
MicroRNA Cancer Regulation
|
| Published in |
Advances in experimental medicine and biology, December 2012
|
| DOI | 10.1007/978-94-007-5590-1_13 |
| Pubmed ID | |
| Book ISBNs |
978-9-40-075589-5, 978-9-40-075590-1
|
| Authors |
Jian-Hua Yang, Liang-Hu Qu |
| Editors |
Ulf Schmitz, Olaf Wolkenhauer, Julio Vera |
| Abstract |
MicroRNAs (miRNAs) are endogenous non-coding RNAs (ncRNAs) of approximately 22 nt that regulate the expression of a large fraction of genes by targeting messenger RNAs (mRNAs). However, determining the biologically significant targets of miRNAs is an ongoing challenge. In this chapter, we describe how to identify miRNA-target interactions and miRNA regulatory networks from high-throughput deep sequencing, CLIP-Seq (HITS-CLIP, PAR-CLIP) and degradome sequencing data using starBase platforms. In starBase, several web-based and stand-alone computational tools were developed to discover Argonaute (Ago) binding and cleavage sites, miRNA-target interactions, perform enrichment analysis of miRNA target genes in Gene Ontology (GO) categories and biological pathways, and identify combinatorial effects between Ago and other RNA-binding proteins (RBPs). Investigating target pathways of miRNAs in human CLIP-Seq data, we found that many cancer-associated miRNAs modulate cancer pathways. Performing an enrichment analysis of genes targeted by highly expressed miRNAs in the mouse brain showed that many miRNAs are involved in cancer-associated MAPK signaling and glioma pathways, as well as neuron-associated neurotrophin signaling and axon guidance pathways. Moreover, thousands of combinatorial binding sites between Ago and RBPs were identified from CLIP-Seq data suggesting RBPs and miRNAs coordinately regulate mRNA transcripts. As a means of comprehensively integrating CLIP-Seq and Degradome-Seq data, the starBase platform is expected to identify clinically relevant miRNA-target regulatory relationships, and reveal multi-dimensional post-transcriptional regulatory networks involving miRNAs and RBPs. starBase is available at http://starbase.sysu.edu.cn/ . |
X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 50% |
| Unknown | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 1 | 50% |
| Members of the public | 1 | 50% |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 8 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Master | 2 | 25% |
| Student > Ph. D. Student | 2 | 25% |
| Student > Doctoral Student | 1 | 13% |
| Professor | 1 | 13% |
| Researcher | 1 | 13% |
| Other | 1 | 13% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 5 | 63% |
| Biochemistry, Genetics and Molecular Biology | 1 | 13% |
| Computer Science | 1 | 13% |
| Medicine and Dentistry | 1 | 13% |