opplncRNA

opplncRNA analyzes long noncoding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) interactions to identify regulatory pathways and competing endogenous RNA (ceRNA) relationships.

Key Features:

• Integration with multiple databases: Incorporates ENCORI, LncBase, miRcode for lncRNA–miRNA interactions and miRcode, ENCORI, TarBase, miRTarBase, miRDB, miRanda, and miRecords for miRNA–mRNA interactions.
• Versatile data input: Processes expression data from microarray and RNA-seq profiling.
• Correlation-based interaction analysis: Calculates interactions from expression profiles using correlation coefficients with user-defined thresholds to identify significant relationships.
• Pathway filtering and validation: Uses integrated database evidence to filter and refine calculated interaction outcomes for biologically supported pathways.
• Network visualization: Visualizes three-layer lncRNA–miRNA–mRNA regulatory networks.

Scientific Applications:

• ceRNA research: Elucidates competing endogenous RNA relationships among lncRNAs, miRNAs, and mRNAs.
• Gene regulation analysis: Identifies putative regulatory interactions affecting gene expression.
• Biomarker and target discovery: Aids identification of candidate biomarkers and potential therapeutic targets based on networked interactions.

Methodology:

Computational steps include calculating correlation coefficients from expression profiles, applying correlation thresholds, filtering interactions using integrated databases (ENCORI, LncBase, miRcode, TarBase, miRTarBase, miRDB, miRanda, miRecords), and visualizing three-layer lncRNA–miRNA–mRNA networks.