Welcome to the RRSM website

RRSM (Relative R Squared Method)

 

    RRSM is an algorithm developed to identify the miRNA (microRNA) target genes. In recent years, many studies have concentrated on the identification of miRNA genes and their mRNA targets. Despite comprehensive exploration of miRNA genes, few miRNA targets have been identified by actual experimental methods. To expedite the identification of miRNA targets for experimental verification, RRSM was established based on miRNA and mRNA microarray profiles to find high-confidence miRNA targets.

 

  

 ◆  References

　• Wang, H. and Li, W. H. (2009). Increasing microRNA target prediction confidence by the relative

        r-squared method. Journal of Theoretical Biology, 259 , 793-798.

    • Wang, H., Wang, YH. and Wu, WS. (2011). Yeast cell cycle transcription factors identification

　    by variable selection criteria.Gene, 485, 172-176 .

    • Hsieh, W.J. and Wang, H. (2011). Human MicroRNA Target Identification by RRSM. Journal

        of Theoretical Biology, 286, 79-84.

    • Hsieh, W.J. and Wang, H. (2013). RRSM with a Data-dependent Threshold for miRNA Target
       Prediction. Journal of Theoretical Biology, 337, 54-60. (code)

    • Wang, H. (2014). Predicting Cancer-Related MiRNAs Using Expression Profiles in Tumor
       Tissue, Current Pharmaceutical Biotechnology, 15(5):438-44.

    • Wang, H.* (2016). Predicting MicroRNA Biomarkers for Cancer using Phylogenetic Tree
       and Microarray Analysis, International Journal of Molecular Sciences, 17, 773.

　

 ◆  Download the R-codes or MATLAB codes

 

 

Download link

File type

File size

Update

R codes

RRSM_R

txt

6.85KB

2013.08.27

MATLAB codes

RRSM_MATLAB

M-file

5.66KB

2013.08.27

R codes

RRSM with a data-dependent threshold

txt

6.96KB

2013.08.27

 

(1)  The R project web for free download is http://www.r-project.org.

(2)  MATLAB software is not free, and MATLAB 7.0 with the statistical toolbox is required to run the codes.

 

Please ensure you already have installed R or MATLAB to run RRSM codes.

　

 ◆  R code user manual.

 ◆  A data Example

     Data source: http://www.psi.toronto.edu/genmir/

     Huang et al., (2007). Using expression profiling data to identify human microRNA targets.
     Nature Methods, 4 , 1045-1049.

 

 

Download link

File type

File size

Update

Data file

DATA

rar

4.64MB

2010.04.21

 

The data include human miRNA and mRNA expression profiles.

X

microarray expression of mRNA (row) across the tissues (column)

Z

microarray expression of microRNA (row) across the tissues (column)

C

NxM binary matrix of indicators of whether a given microRNA putatively targets a given mRNA.
     - M: Number of microRNAs
     - N: Number of mRNAs

tissues

tissue labels

glbl_HGNC

mRNA identifiers in HGNC

glbl_EMBL

mRNA identifiers in EMBL

mlbl

microRNA identifiers

 

 

 

 

 

 

 

 

 

 

 

 ◆  Note

(1)  The s and p0 thresholds can be selected according to training data.

(2)  The normalized or non-normalized procedure can be chosen.  

(3)  To analyze your own data, the data must be saved in .xls format.

 

 ◆  Contact

     If you have any questions on RRSM codes, please feel free to contact us at hsiuyingwang@nctu.edu.tw (Primary) ;
    wang@stat.nctu.edu.tw  (Secondary). We welcome your feedback and comments.