CircRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging.

ABSTRACT:

Motivation

Circular RNAs (circRNAs) are long noncoding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs.

Results

We developed circRNA-sponging, a nextflow pipeline that (i) identifies circRNAs via backsplicing junctions detected in RNA-seq data, (ii) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (iii) performs differential expression analysis, (iv) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data,

SUBMITTER: Hoffmann M 

PROVIDER: S-EPMC10359604 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature