mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets

被引：66

作者：

Ritchie, William ^{[1
]}

Flamant, Stephane ^{[1
]}

Rasko, John E. J. ^{[1
,2
]}

机构：

[1] Univ Sydney, Centenary Inst, Gene & Stem Cell Therapy Program, Sydney, NSW 2042, Australia

[2] Royal Prince Alfred Hosp, Sydney Canc Ctr, Camperdown, NSW 2050, Australia

来源：

BIOINFORMATICS | 2010年 / 26卷 / 02期

基金：

英国医学研究理事会;

关键词：

GENE-EXPRESSION; MICROARRAY;

D O I：

10.1093/bioinformatics/btp649

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: microRNAs (miRNAs) are short non-coding RNAs that regulate gene expression by inhibiting target mRNA genes. Their tissue-and disease-specific expression patterns have immense therapeutic and diagnostic potential. To understand these patterns, a reliable compilation of miRNA and mRNA expression data is required to compare multiple tissue types. Moreover, with the appropriate statistical tools, such a resource could be interrogated to discover functionally related miRNA-mRNA pairs. Results: We have developed mimiRNA, an online resource that integrates expression data from 1483 samples and permits visualization of the expression of 635 human miRNAs across 188 different tissues or cell types. mimiRNA incorporates a novel sample classification algorithm, ExParser, that groups identical miRNA or mRNA experiments from separate sources. This enables mimiRNA to provide reliable expression profiles and to discover functional relations between miRNAs and mRNAs such as miRNA targets. Additionally, mimiRNA incorporates a decision tree algorithm to discover distinguishing miRNA features between two tissue or cell types. We validate the efficacy of our resource on independent experimental data and through biologically relevant analyses.

引用

页码：223 / 227

页数：5