RSNET

RSNET (Redundancy Silencing and Network Enhancement Technique) is a computational method to infer gene regulatory networks (GRNs) from gene expression data. The main goal of RSNET is to filter out indirect interactions and retain direct ones, thereby improving the accuracy of the inferred networks.

Key points:

1. GRN inference methods often predict many indirect interactions, making identifying the true direct interactions challenging.

2. RSNET addresses this issue by silencing redundant interactions, including weak and indirect connections, through recursive optimization.

3. The method also constrains highly dependent nodes in the model to preserve real interactions.

4. The performance of RSNET was assessed using simulation studies, DREAM challenge datasets, and the Escherichia coli network. The results showed that RSNET outperformed other methods regarding sensitivity and accuracy.

5. As a case study, RSNET was applied to construct a functional GRN for apple fruit ripening using gene expression data.

Topic

Molecular interactions, pathways and networks;Gene expression;Mathematics

Detail

  • Operation: Gene regulatory network prediction;Gene regulatory network analysis;Pathway analysis

  • Software interface: Library

  • Language: MATLAB

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: National Natural Science Foundation of China, Technology Innovation Zone Project, and CAS Pioneer Hundred Talents Program.

  • Input: -

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique.
  • Jiang X and Zhang X. RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique. RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique. 2022; 23:165. doi: 10.1186/s12859-022-04696-w
  • https://doi.org/10.1186/S12859-022-04696-W
  • PMID: 35524190
  • PMC: PMC9074326

Download and documentation

< Back to DB search