spongeScan

spongeScan identifies and visualizes microRNA response elements (MREs) in long non-coding RNAs (lncRNAs) to predict putative miRNA sponge (ceRNA) activity.

Key Features:

• Identification of MREs: Predicts microRNA response elements within lncRNA sequences with a focus on sites relevant to competitive endogenous RNA (ceRNA) activity.
• Visualization of MREs: Provides graphical representation of putative MRE locations, spatial distribution, and site density along lncRNA sequences.
• Assessment Metrics: Computes quantitative measures to evaluate the likelihood that a given lncRNA can act as a miRNA sponge.

Scientific Applications:

• Gene Expression Regulation: Infers how lncRNAs may modulate gene expression by sequestering miRNAs and altering miRNA availability for mRNA targets.
• Pathway Analysis: Enables investigation of ceRNA involvement in biological pathways and diseases where miRNA regulation is critical.
• Functional Annotation: Supports annotation of lncRNAs with potential regulatory roles based on predicted miRNA-lncRNA interactions.

Methodology:

Predicts MREs within lncRNAs using sequence analysis and integrates visualization of predicted sites, explicitly addressing prediction challenges specific to lncRNA sequences rather than mRNA targets.