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Open Access Highly Accessed Methodology article

miRAS: a data processing system for miRNA expression profiling study

Feng Tian123, Huayue Zhang23, Xinyu Zhang23, Chi Song13, Yongjing Xia2, Yiqing Wu2 and Xiangjun Liu123*

Author Affiliations

1 Department of Biological Science and Biotechnology, Tsinghua University, Beijing 100084, People's Republic of China

2 Institutes of Biomedicine, Tsinghua University, Beijing 100084, People's Republic of China

3 Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, People's Republic of China

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BMC Bioinformatics 2007, 8:285  doi:10.1186/1471-2105-8-285

Published: 4 August 2007

Abstract

Background

The study of microRNAs (miRNAs) is attracting great considerations. Recent studies revealed that miRNAs play as important regulators of gene expression and some even as cancer players or inhibitors. Many studies try to discover new miRNAs and reveal the miRNA expression profile in cancer using a SAGE-based total RNA clone method. However, the data processing of this method is labor-intensive with several different biological databases and more than ten data processing steps involved.

Results

With miRAS, miRNAs and possible miRNA candidates contained in the submitted sequencing data were obtained together with their expression profile. The functions of known and predicted miRNAs were then analyzed by miRNA target prediction followed by target gene annotations. Finally, to extract the biological significance of the miRNAs in the samples, further annotations of the known miRNA and target genes were performed by collecting the public expression datasets of miRNA and target genes in normal and cancer tissues.

Conclusion

We introduce a web-based analysis platform called miRNA Analysis System (miRAS), for processing and analyzing of the sequence data obtained from the total RNA clone method. The system was built on generalizing the study of a liver cancer cell line total RNA sequencing project. miRAS is freely available on the web.