Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
Department of Human Anatomy, Histology & Embryology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
Genomics Proteomics Bioinformatics. 2022 Jun;20(3):549-556. doi: 10.1016/j.gpb.2021.01.003. Epub 2021 Feb 23.
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.
环状 RNA（circRNAs）参与多种生物过程和疾病发病机制。然而，在数以万计的 circRNA 中，只有少数功能性 circRNAs 被鉴定出来，部分原因是目前大多数方法都是基于环状连接计数，而忽略了环状 RNA 是通过反向剪接（BS）从宿主基因形成的事实。为了区分源自 BS 或宿主基因的表达差异，我们提出了差异表达的反向剪接（DEBKS），这是一种软件程序，可以简化两个 rRNA 耗尽的 RNA 测序（RNA-seq）样本组之间差异 BS 事件的发现。通过应用于真实和模拟数据，并采用 RT-qPCR 进行验证，我们证明 DEBKS 能够有效地和准确地检测配对和非配对样本组之间具有差异 BS 事件的 circRNAs。DEBKS 可在 https://github.com/yangence/DEBKS 上作为开源软件获得。
