DEBKS: A Tool to Detect Differentially Expressed Circular RNAs

Abstract

Circular RNAs (circRNAs) are involved in various biological processes and disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that a circRNA is formed from the host gene by back-splicing (BS). To distinguish the expression difference originating from BS or the host gene, we present differentially expressed back-splicing (DEBKS), a software program to streamline the discovery of differential BS events between two rRNA-depleted RNA sequencing (RNA-seq) sample groups. By applying to real and simulated data and employing RT-qPCR for validation, we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups. DEBKS is available at https://github.com/yangence/DEBKS as open-source software.

CircSV2b participates in oxidative stress regulation through miR-5107-5p-Foxk1-Akt1 axis in Parkinson's disease

“…In this study, we performed rRNA-depleted RNA-seq on SNpc and STR tissues and paired control tissues from a PD mouse model. Then, we analyzed the data using CIRI2 [ 14 ], CIRCexplorer2 [ 15 ], and DEBKS [ 16 ] software. Differentially expressed circRNAs (DECs) were screened out.…”

Systematic benchmarking of statistical methods to assess differential expression of circular RNAs

“…We collected an unprecedented and extensive set of DEMs by selecting tools available as R packages, currently maintained and functioning, reasonably fast, and well-performing or never tested in previous benchmarks. We did not consider statistical models devised to assess the variation of the circular-tolinear expression ratio (CLR), such as CircTest [59], seekCRIT [60], DEBKS [61], and the circMeta test for CLR [22], because they address a problem distinct from differential circRNA abundance.…”

CircRNA-Pro: A Novel Toolkit for High-Precision Detection of Differentially Expressed Circular RNAs and Translatable Circular RNAs

“…CircRNAs were identified by detecting reads with reverse splicing junctions, using the aligned reads data. Following circRNAs identification, we used a suite of tools including Ciriquant [37], CircTest [39] and DEBKS [38] to detect differentially expressed circRNAs between samples. The expression levels of differentially expressed circRNAs identified by these tools across various samples were visualized using the Pheatmap package.…”

“…Currently, there are numerous software tools available for the detection of circRNAs (e.g., CIRI2 [34], CIRCexplorer2 [35], CirComPara2 [36]). However, there is a limited number of tools specifically designed for the detection of differentially expressed circRNAs, with CIRIquant [37], DEBKS [38], and Circtest [39] being the primary options.…”

“…Currently, there are numerous software tools available for the detection of circRNAs (e.g., CIRI2[34], CIRCexplorer2 [35], CirComPara2 [36]). However, there is a limited number of tools specifically designed for the detection of differentially expressed circRNAs, with CIRIquant [37], DEBKS [38], and Circtest [39] being the primary options. Due to the utilization of different algorithms, these tools often produce inconsistent results [32, 38], making it more challenging to accurately identify differentially expressed circRNAs.…”