lncRNAfunc

lncRNAfunc annotates functional interactions and regulatory mechanisms of long non-coding RNAs (lncRNAs) in human cancer by integrating TCGA data to characterize lncRNA interactions with DNA, RNA, and proteins.

Key Features:

• Extensive LncRNA Collection: Contains 15,900 lncRNAs across 33 human cancer types sourced from The Cancer Genome Atlas (TCGA).
• Multifaceted Interaction Analyses: Performs interaction analyses at DNA, RNA, and protein levels to reveal how lncRNAs coordinate with other biomolecules.
• Mechanistic Insights into Gene Regulation: Annotates potential mechanisms including binding to enhancers and 3'-UTRs, competition with mRNAs for miRNA-binding sites, and recruitment of transcription factors to promoters.
• Alternative Splicing Influence: Investigates lncRNA interactions with RNA-binding proteins to assess effects on alternative splicing.
• Functional Annotations: Provides annotations linking lncRNAs to cancer stages, RNA A-to-I editing events, and expression quantitative trait loci (eQTLs).

Scientific Applications:

• Therapeutic Target Identification: Catalogs therapeutically targetable lncRNAs and their regulatory interactions to support identification of cancer treatment targets.
• Research Resource: Serves as a comprehensive reference for studying regulatory roles of lncRNAs in oncogenesis and tumor progression.

Methodology:

Integrates TCGA datasets with advanced bioinformatics techniques to perform systematic interaction analyses and functional annotations, including DNA/RNA/protein-level interaction analysis, enhancer and 3'-UTR binding, miRNA competition, transcription factor recruitment, RNA-binding protein interaction analysis, RNA A-to-I editing annotation, eQTL mapping, and alternative splicing analysis.