BioVLAB-MMIA-NGS: microRNA-mRNA Integrated Analysis Using High-Throughput Sequencing Data

Bioinformatics. 2015 Jan 15;31(2):265-7. doi: 10.1093/bioinformatics/btu614. Epub 2014 Sep 29.

Abstract

Motivation: It is now well established that microRNAs (miRNAs) play a critical role in regulating gene expression in a sequence-specific manner, and genome-wide efforts are underway to predict known and novel miRNA targets. However, the integrated miRNA-mRNA analysis remains a major computational challenge, requiring powerful informatics systems and bioinformatics expertise.

Results: The objective of this study was to modify our widely recognized Web server for the integrated mRNA-miRNA analysis (MMIA) and its subsequent deployment on the Amazon cloud (BioVLAB-MMIA) to be compatible with high-throughput platforms, including next-generation sequencing (NGS) data (e.g. RNA-seq). We developed a new version called the BioVLAB-MMIA-NGS, deployed on both Amazon cloud and on a high-performance publicly available server called MAHA. By using NGS data and integrating various bioinformatics tools and databases, BioVLAB-MMIA-NGS offers several advantages. First, sequencing data is more accurate than array-based methods for determining miRNA expression levels. Second, potential novel miRNAs can be detected by using various computational methods for characterizing miRNAs. Third, because miRNA-mediated gene regulation is due to hybridization of an miRNA to its target mRNA, sequencing data can be used to identify many-to-many relationship between miRNAs and target genes with high accuracy.

Availability and implementation: http://epigenomics.snu.ac.kr/biovlab_mmia_ngs/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Database Management Systems
  • Databases, Genetic
  • Gene Expression Regulation
  • Genome, Human
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • MicroRNAs / genetics
  • MicroRNAs / metabolism*
  • RNA / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Sequence Analysis, RNA / methods*
  • User-Computer Interface

Substances

  • MicroRNAs
  • RNA, Messenger
  • RNA