OmicShare

OmicShare performs comprehensive analysis of competing endogenous RNA (ceRNA) networks to investigate lncRNA-mediated gene regulation and prognostic associations in cancer.

Key Features:

• Integration with Major Databases: Leverages The Cancer Genome Atlas (TCGA), DIANA-TarBase, and TargetScan to supply expression data and predicted/validated miRNA–target interactions for ceRNA network construction.
• Identification of Dysregulated lncRNAs: Detects dysregulated long non-coding RNAs (lncRNAs) from RNA-seq data to pinpoint candidates for downstream analysis.
• Survival Analysis: Applies Kaplan–Meier survival analysis to associate lncRNA expression with patient outcomes and identify survival-associated lncRNAs.
• ceRNA Network Construction: Builds ceRNA networks connecting lncRNAs, miRNAs, and mRNAs using DIANA-TarBase and TargetScan interaction data.
• Pathway and Functional Analysis: Performs Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses to assess biological roles of network components.
• Visualization Capabilities: Produces visual representations of ceRNA networks to support interpretation of interactions among lncRNAs, miRNAs, and mRNAs.

Scientific Applications:

• NSCLC (LUAD and LUSC) lncRNA discovery: Identifies dysregulated lncRNAs in non-small cell lung cancer using TCGA RNA-seq data.
• Prognostic biomarker identification: Determines survival-associated lncRNAs via Kaplan–Meier analysis to nominate potential prognostic markers.
• ceRNA network analysis centered on specific lncRNAs: Constructs networks centered on lncRNAs such as CASC8, LINC01842, and VPS9D1-AS1 to explore interactions with miRNAs and mRNAs.
• Functional interpretation of lncRNA-mediated regulation: Uses GO and KEGG analyses to infer biological pathways and functions linked to identified lncRNAs within ceRNA networks.

Methodology:

Utilizes RNA-seq data from TCGA to identify dysregulated lncRNAs; applies Kaplan–Meier survival analysis for prognostic association; constructs ceRNA networks using DIANA-TarBase and TargetScan interaction data; conducts GO and KEGG pathway analyses for functional interpretation.