CeRNASeek

CeRNASeek identifies and analyzes competitive endogenous RNA (ceRNA) interactions by integrating miRNA–mRNA regulation and heterogeneous multi-omics data to characterize ceRNA-ceRNA regulatory relationships.

Key Features:

• Identification methods: Incorporates six computational approaches, comprising two global prediction methods and four context-specific prediction methods, for identifying ceRNA-ceRNA interactions.
• Data modality: Applies prediction methods using miRNA–mRNA regulation data alone or by integrating heterogeneous omics data sources.
• Multi-omics integration: Integrates diverse omics data to inform context-specific ceRNA predictions.
• Regulatory network analysis: Performs regulatory network analysis on predicted ceRNA-ceRNA pairs to explore interaction topology and pathways.
• Functional annotation analysis: Performs functional annotation of identified ceRNA relationships to assess biological implications.
• Survival prognosis analysis: Performs survival prognosis analysis based on expression levels of ceRNA ternary pairs to evaluate associations with patient outcomes.

Scientific Applications:

• ceRNA function in complex diseases: Enables investigation of ceRNA-mediated regulation in physiological and pathological processes, including complex diseases.
• Cancer-related ceRNA prioritization: Supports prioritization of candidate regulatory RNAs implicated in oncogenesis based on predicted ceRNA interactions.
• Cancer subtyping: Facilitates cancer subtyping using ceRNA expression and interaction profiles.

Methodology:

Employs six computational prediction approaches (two global, four context-specific) applied to miRNA–mRNA regulation data or integrated heterogeneous omics data, and conducts regulatory network, functional annotation, and survival prognosis analyses on predicted ceRNA-ceRNA pairs.