Using expression profiling to identify human microRNA targets

Jim C. Huang1,6, Tomas Babak2,6, Timothy W. Corson2,3, Gordon Chua4, Sofia Khan2,3, Brenda L. Gallie2,3, Timothy R. Hughes2,4,
Benjamin J. Blencowe2,4, Brendan J. Frey1,4,5,7 and Quaid D. Morris2,4,5,7

1 Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Rd., Toronto, ON, M5S 3G4, Canada
2 Department of Molecular and Medical Genetics, University of Toronto, 1 King's College Rd., Toronto, ON, M5S 1A8, Canada
3 Division of Applied Oncology, Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, ON, M5G 2M9, Canada
4 Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, 160 College St., M5G 1L6, Canada
5 Department of Computer Science, University of Toronto, 10 King's College Rd., M5S 3G4, Canada
6 These authors contributed to this work equally
7 To whom correspondence should be addressed:,

Frequently asked questions

Q: Where can I find the expression data sets used in the paper?

A: Microarray data sets are available at NCBI GEO (GEO Accession: GSE7072 (microRNA) and GSE7185 (mRNA)). The GSE7072 data set is the microRNA expression data shown in Figure 2A of the paper. The GSE7185 data set is the mRNA expression data used in tandem with mRNA sequence to find enriched motifs and generate Figure 3A of the paper.
The mRNA and microRNA expression data sets used to find functional microRNA-target interactions can be downloaded in MATLAB format (requires MATLAB v7.0 or above) at The files are provided sparately or together in one zip file. The mRNA and miRNA expression data sets used to find functional miRNA-target interactions is miRdata_Golub_TSS_human.mat. The output of GenMiR++ is stored in GenMiRout_Golub_TSS_human.mat.

Q: What do the fields in the MATLAB file for the mRNA and miRNA expression data correspond to?

A: The MATLAB files contain these different fields:
Other fields are explained in this Supplementary Description.

Q: I'd like to re-run the analyses presented in the paper. How do I go about it?

A: In order to reproduce the results and plots shown in the paper, please follow these steps:

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