Analyzing high-throughput sequencing data for profiling microRNA expression


MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation in both animals and plants.

Expression profiling by microarray is one high-throughput and robust method for detecting miRNA expression, however, the approach is restricted to detecting the expression of known miRNAs. RNA-Seq is a promising new method with high sensitivity and specificity and can be used not only to measure the abundance of small-RNA sequences in a sample but also to discover novel miRNAs.

miRExpress is a stand-alone software package is implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. The software is also a database-supported, efficient and flexible tool for investigating miRNA regulation.

The software is freely available at:

  • Wang, W.C., et al., (2009) miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics 10(1), 328. [article]