Contents

1 Overview

1.1 Background

  • MicroRNAs (miRNAs) regulate most cellular processes and are promising therapeutic candidates for cancer and other diseases.
  • Understanding miRNA function is challenging due to the “many-to-many” relationships between miRNAs and their target genes.
  • In addition, complex interplay exists between miRNAs and other functional elements, such as transcription factors, lncRNAs, etc.
  • Network-based approach enables the integration of multiple data types and interpreting results at a systems level to allow the understanding of miRNA corporative functions and regulatory mechanisms.

1.2 Overall goal

To provide an easy-to-use web application to enable complex miRNA-centric network analytics for systems-level interpretation of miRNA functions and gene regulations.

1.3 New features in miRNet 2.0

The miRNet 1.0 was mainly about miRNA–target gene network. The miRNet 2.0 has expanded to include other key players involved in gene regulatory network with new modules, new knowledge bases and new visualization algorithms to support multipartite network creation, analysis and exploration

  1. Added support for miRNA family mapping and enrichment analysis
  2. Added support for tissue and exosomal specific miRNA annotation
  3. Added support for more species based on user’s feedback
  4. Added two modules to support xeno-miRNA targets exploration & visualization
  5. Added a new module to support miRNA-TF regulatory network
  6. Added a new module to support miR-SNP annotation and target interactions
  7. Added a new module to support integrating multiple types of molecules for systemslevel visual analytics
  8. Added additional network layout algorithms, including bipartite/tripartite, concentric and backbone layout
  9. Significantly expanded miRNA interaction knowledgebase
  10. Revamped the web interface, optimized the workflow, and introduced microservices and web application programming interface (API)

1.4 miRNet & its knowledgebase

1.5 Workflow

1.6 Network analysis