SeedMatchR

SeedMatchR detects seed-mediated off-target effects of siRNAs in RNA-seq differential expression data by identifying miRNA-like seed matches in mRNA 3' untranslated regions.

Key Features:

• Detection of Seed-Mediated Off-Target Effects: Detects siRNA sequences with approximately 8-nucleotide seed regions at the 5' end of the guide strand that can match 3' UTRs of mRNAs and produce miRNA-like regulatory effects.
• Integration with Differential Expression Tools: Annotates differential expression results from tools such as DESeq2 with predicted seed matches to attribute cumulative gene expression changes to siRNA seed activity.
• Visualization Capabilities: Visualizes seed-match annotations together with differential expression patterns to facilitate interpretation of potential off-target interactions.

Scientific Applications:

• siRNA knockdown experiments: Identifies and distinguishes seed-mediated off-target regulation in RNA-seq analyses of siRNA knockdown studies.
• Functional genomics and therapeutic research: Reveals miRNA-like off-target gene regulation to improve interpretation of gene expression changes relevant to functional genomics and therapeutic siRNA assessment.

Methodology:

Annotates differential expression outputs (e.g., from DESeq2) with predicted siRNA seed matches to 3' UTRs and leverages publicly available RNA-seq data to detect and visualize seed-mediated changes in gene expression.