title: miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression.
abstract: BACKGROUND
  MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation in both animals and plants. In the last few years, the oligonucleotide microarray is one high-throughput and robust method for detecting miRNA expression. However, the approach is restricted to detecting the expression of known miRNAs. Second-generation sequencing is an inexpensive and high-throughput sequencing method. This new method is a promising tool with high sensitivity and specificity and can be used to measure the abundance of small-RNA sequences in a sample. Hence, the expression profiling of miRNAs can involve use of sequencing rather than an oligonucleotide array. Additionally, this method can be adopted to discover novel miRNAs.
  
  
  RESULTS
  This work presents a systematic approach, miRExpress, for extracting miRNA expression profiles from sequencing reads obtained by second-generation sequencing technology. 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. Moreover, we demonstrate the utility of miRExpress in extracting miRNA expression profiles from two Illumina data sets constructed for the human and a plant species.
  
  
  CONCLUSIONS
  We develop miRExpress, which is a database-supported, efficient and flexible tool for detecting miRNA expression profile. The analysis of two Illumina data sets constructed from human and plant demonstrate the effectiveness of miRExpress to obtain miRNA expression profiles and show the usability in finding novel miRNAs.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan, Republic of China. canser.bi95g@nctu.edu.tw
authors.forename: Wei-Chi
authors.initials: WC
authors.lastname: Wang
authors.forename: Feng-Mao
authors.initials: FM
authors.lastname: Lin
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Chang
authors.forename: Kuan-Yu
authors.initials: KY
authors.lastname: Lin
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
authors.forename: Na-Sheng
authors.initials: NS
authors.lastname: Lin
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D015894:Genome, Human; D018745:Genome, Plant; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs