TY - JOUR
T1 - MiRExpress
T2 - Analyzing high-throughput sequencing data for profiling microRNA expression
AU - Wang, Wei Chi
AU - Lin, Feng Mao
AU - Chang, Wen Chi
AU - Lin, Kuan Yu
AU - Huang, Hsien Da
AU - Lin, Na Sheng
N1 - Funding Information:
The authors thank the National Science Council of the Republic of China for financially supporting this research under Contracts No. NSC 98-2311-B-009-004-MY3 and NSC 98-2627-B-009-005. Special thanks to the National Research Program for Genomic Medicine (NRPGM), Taiwan, for financial support. This work was also supported in part by MOE ATU. Funding to pay the Open Access publication charges for this article was provided by the National Science Council of the Republic of China and MOE ATU.
PY - 2009/10/12
Y1 - 2009/10/12
N2 - 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. Conclusion: 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.
AB - 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. Conclusion: 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.
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U2 - 10.1186/1471-2105-10-328
DO - 10.1186/1471-2105-10-328
M3 - Article
C2 - 19821977
AN - SCOPUS:70449639806
SN - 1471-2105
VL - 10
SP - 328
JO - BMC Bioinformatics
JF - BMC Bioinformatics
M1 - 1471
ER -