Mirsynergy

The software tool 'Mirsynergy' is a deterministic overlapping clustering algorithm designed to identify microRNA regulatory modules (MiRMs) for deciphering aberrant transcriptional regulatory networks in cancer. The algorithm forms MiRMs based on co-occurring microRNA targets and expands each MiRM by greedily including or excluding mRNAs to maximize the synergy score. Using expression data from ovarian, breast, and thyroid cancer, the algorithm was compared with internal controls and existing methods, and the results showed that Mirsynergy-MiRMs exhibit significantly higher functional enrichment and more coherent miRNA-mRNA expression anti-correlation.

Topic

Gene transcripts;RNA;Functional, regulatory and non-coding RNA

Detail

  • Operation: Transcriptional regulatory element prediction

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: GNU General Public License v2

  • Cost: Free

  • Version name: 1.18.0

  • Credit: Natural Sciences and Engineering Research Council (NSERC) Canada Graduate Scholarship, Ontario Research Fund - Global Leader (Round 2), NSERC, the National Natural Science Foundation of China, Hunan Provincial Natural Science Foundation of China.

  • Input: -

  • Output: -

  • Contact: Yue Li yueli@cs.toronto.edu

  • Collection: -

  • Maturity: Stable

Publications

  • Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion.
  • Li Y, et al. Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. 2014; 30:2627-35. doi: 10.1093/bioinformatics/btu373
  • https://doi.org/10.1093/bioinformatics/btu373
  • PMID: 24894504
  • PMC: -

Download and documentation

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