Using miRNA-mRNA and gene-gene interaction matrices, form miRNA regulatory module (MiRM), where miRNA or mRNA can participate in more than one module and the number of modules are automatically determined by the running of the algorithm. The underlying algorithm of Mirsynergy is an adaptation of a recently clustering algorithm called ClusterONE (Cluster by Overlapping Neighborhood Expansion) by Nepusz et al. (2012)

‣ Mirsynergy R/Bioconductor package:

R binary package is available at Bioconductor

Install (in terminal):

    R CMD INSTALL Mirsynergy_0.99.2.tar.gz

Usage (in R environment):

1. • Load Mirsynergy:
   

2. -library(Mirsynergy)
   

1. • Help/Manual:
   

2. -?Mirsynergy: Mirsynergy-manual.pdf
   

3. -vignette(“Mirsynergy”): Mirsynergy.pdf;
   

4. -demo code: Mirsynergy.R
   

‣ Full datasets used in the manuscript:

1. •Ovarian cancer data: ov0.RData, ov0_ggi.RData
   

2. •Breast cancer data: brca.RData, brca_ggi.RData
   

3. •Thyroid cancer data: thca.RData, thca_ggi.RData
   

NB: We can follow the second example in the above vignette using the full data instead of the test data to construct the full MiRM for breast and thyroid cancer. The entire process will take ~2 hours.

Citation:

1. •Manuscript in preparation
   

Other References:

1. •Nepusz, T., Yu, H., & Paccanaro, A. (2012). Detecting overlapping protein complexes in protein-protein interaction networks. Nature Methods, 9(5), 471-472. doi:10.1038/nmeth.1938