mirTarCLASH

mirTarCLASH deposits and organizes 502,061/322,707/224,452 unique hybrid reads from human/mouse/worm miRNA chimeric read-based experiments to facilitate exploration of miRNA-target pairs and binding sites with confidence evaluation filters and transcript atlas visualization.

Key Features:

• Chimeric read processing: The chimera analysis algorithm ChiRA is adopted to analyze miRNA-target pairs derived from CLASH-like experiments.
• Binding site inference: Two distinct binding site inference tools, RNAup and miRanda, are used to predict miRNA binding sites.
• Confidence evaluation filters: Results can be refined based on read depths, numbers of supporting algorithms, and cross-linking-induced mutations to enhance confidence levels.
• Transcript atlas visualization: miRNA-binding sites are visually represented through an integrated transcript atlas.

Scientific Applications:

• miRNA-target interaction analysis: Supports investigation of miRNA-target gene pairs and their corresponding binding sites extracted from chimeric reads.
• Binding site characterization: Enables exploration of key properties of miRNA targeting sites including read depths, supporting algorithms, and cross-linking-induced mutations.
• Experimental research design: Provides novel insights for subsequent experimental research designs, as demonstrated by the well-characterized interaction between cel-let-7-5p and lin-41 in Caenorhabditis elegans.

Methodology:

mirTarCLASH adopts the chimera analysis algorithm ChiRA and two distinct binding site inference tools, RNAup and miRanda, to analyze miRNA-target pairs and binding sites from CLASH-seq and CLASH-like experiments.