miRAS: a data processing system for miRNA expression profiling study.
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.


CONCLUSIONS
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.
Tian
Feng
F
Department of Biological Science and Biotechnology, Tsinghua University, Beijing, People's Republic of China. tianfeng@mails.tsinghua.edu.cn <tianfeng@mails.tsinghua.edu.cn>
Zhang
Huayue
H
Zhang
Xinyu
X
Song
Chi
C
Xia
Yongjing
Y
Wu
Yiqing
Y
Liu
Xiangjun
X
D000465:Algorithms; D001483:Base Sequence; D003001:Cloning, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D020407:Internet; D008969:Molecular Sequence Data; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D012313:RNA