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mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer

Chao Cheng1, Xuping Fu2, Pedro Alves1 and Mark Gerstein134*

Author Affiliations

1 Program in Computational Biology and Bioinformatics, Yale University, George Street, New Haven, CT 06511, USA

2 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Handan Road, Yangpu District, Shanghai, 200433, PR China

3 Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue, New Haven, CT 06520, USA

4 Department of Computer Science, Yale University, Prospect Street, New Haven, CT 06511, USA

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Genome Biology 2009, 10:R90  doi:10.1186/gb-2009-10-9-r90

Published: 1 September 2009



Recent studies have shown that the regulatory effect of microRNAs can be investigated by examining expression changes of their target genes. Given this, it is useful to define an overall metric of regulatory effect for a specific microRNA and see how this changes across different conditions.


Here, we define a regulatory effect score (RE-score) to measure the inhibitory effect of a microRNA in a sample, essentially the average difference in expression of its targets versus non-targets. Then we compare the RE-scores of various microRNAs between two breast cancer subtypes: estrogen receptor positive (ER+) and negative (ER-). We applied this approach to five microarray breast cancer datasets and found that the expression of target genes of most microRNAs was more repressed in ER- than ER+; that is, microRNAs appear to have higher RE-scores in ER- breast cancer. These results are robust to the microRNA target prediction method. To interpret these findings, we analyzed the level of microRNA expression in previous studies and found that higher microRNA expression was not always accompanied by higher inhibitory effects. However, several key microRNA processing genes, especially Ago2 and Dicer, were differentially expressed between ER- and ER+ breast cancer, which may explain the different regulatory effects of microRNAs in these two breast cancer subtypes.


The RE-score is a promising indicator to measure microRNAs' inhibitory effects. Most microRNAs exhibit higher RE-scores in ER- than in ER+ samples, suggesting that they have stronger inhibitory effects in ER- breast cancers.