ceRNAnetsim

'ceRNAnetsim' introduces a network-based model for exploring competing endogenous RNA (ceRNA) regulations and crosstalk within human non-coding RNA interactions. The model incorporates miRNA:ceRNA interactions with expression values, enabling the calculation of network-wide effects resulting from perturbations in node expression levels. It considers miRNA interaction factors such as seed type and binding energy. Analysis of large-scale miRNA: target networks in breast cancer patients using this approach identified highly perturbing genes, aligning with breast cancer-associated genes and miRNAs. The tool is scalable and can incorporate emerging miRNA effectors like circRNAs and lncRNAs.