INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA.

IF 4.4 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Bioinformatics Pub Date : 2023-09-02 DOI:10.1093/bioinformatics/btad569

Jace Webster, Hung Mai, Amy Ly, Christopher Maher

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引用次数: 0

Abstract

Motivation: Backsplicing of RNA results in circularized rather than linear transcripts, known as circular RNA (circRNA). A recently discovered and poorly understood subset of circRNAs that are composed of multiple genes, termed fusion-derived circular RNAs (fcircRNAs), represent a class of potential biomarkers shown to have oncogenic potential. Detection of fcircRNAs eludes existing analytical tools, making it difficult to more comprehensively assess their prevalence and function. Improved detection methods may lead to additional biological and clinical insights related to fcircRNAs.

Results: We developed the first unbiased tool for detecting fcircRNAs (INTEGRATE-Circ) and visualizing fcircRNAs (INTEGRATE-Vis) from RNA-Seq data. We found that INTEGRATE-Circ was more sensitive, precise and accurate than other tools based on our analysis of simulated RNA-Seq data and our tool was able to outperform other tools in an analysis of public lymphoblast cell line data. Finally, we were able to validate in vitro three novel fcircRNAs detected by INTEGRATE-Circ in a well-characterized breast cancer cell line.

Availability and implementation: Open source code for INTEGRATE-Circ and INTEGRATE-Vis is available at https://www.github.com/ChrisMaherLab/INTEGRATE-CIRC and https://www.github.com/ChrisMaherLab/INTEGRATE-Vis.

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整合Circ和整合Vis：融合衍生的环状RNA的无偏检测和可视化。

动机：RNA的反转录产生环状而非线性转录物，称为环状RNA（circRNA）。最近发现的一种由多个基因组成的circRNA亚群，称为融合衍生的环状RNA（fcircRNA），代表了一类具有致癌潜力的潜在生物标志物。现有的分析工具无法检测fcircRNA，因此很难更全面地评估其患病率和功能。改进的检测方法可能会带来与fcircRNA相关的额外生物学和临床见解。结果：我们开发了第一个从RNA-Seq数据中检测fcircRNA（INTEGRATE Circ）和可视化fcircRNAs（INTEGIATE Vis）的无偏工具。基于我们对模拟RNA-Seq数据的分析，我们发现INTEGRATE Circ比其他工具更灵敏、更精确、更准确，并且我们的工具在分析公共淋巴母细胞系数据方面能够优于其他工具。最后，我们能够在体外验证在一个特征良好的乳腺癌症细胞系中通过INTEGRATE-Circ检测到的三种新型fcircRNA。可用性和实现：INTEGRATE Circ和INTEGRATE-Vis的开源代码可在https://www.github.com/ChrisMaherLab/INTEGRATE-CIRC和https://www.github.com/ChrisMaherLab/INTEGRATE-Vis.

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来源期刊

Bioinformatics 生物-生化研究方法

CiteScore

11.20

自引率

5.20%

发文量

753

审稿时长

2.1 months

期刊介绍： The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.