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In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Published on: October 21, 2022

CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers

Yigang Chen^1,2,3, Lantian Yao^3,4, Yun Tang^2,3

¹The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong Province 518172, China.

Nucleic Acids Research

|December 1, 2021

Abstract:

Circular RNAs (circRNAs), which are single-stranded RNA molecules that have individually formed into a covalently closed continuous loop, act as sponges of microRNAs to regulate transcription and translation. CircRNAs are important molecules in the field of cancer diagnosis, as growing evidence suggests that they are closely related to pathological cancer features. Therefore, they have high potential for clinical use as novel cancer biomarkers. In this article, we present our updates to CircNet (version 2.0), into which circRNAs from circAtlas and MiOncoCirc, and novel circRNAs from The Cancer Genome Atlas database have been integrated. In total, 2732 samples from 37 types of cancers were integrated into CircNet 2.0 and analyzed using several of the most reliable circRNA detection algorithms. Furthermore, target miRNAs were predicted from the full-length circRNA sequence using three reliable tools (PITA, miRanda and TargetScan). Additionally, 384 897 experimentally verified miRNA-target interactions from miRTarBase were integrated into our database to facilitate the construction of high-quality circRNA-miRNA-gene regulatory networks. These improvements, along with the user-friendly interactive web interface for data presentation, search, and visualization, showcase the updated CircNet database as a powerful, experimentally validated resource, for providing strong data support in the biomedical fields. CircNet 2.0 is currently accessible at https://awi.cuhk.edu.cn/∼CircNet.

Insights

Circular RNAs (circRNAs) are key cancer biomarkers. The updated CircNet 2.0 database integrates extensive circRNA data, offering a powerful resource for cancer research and clinical applications.

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Circular RNAs (circRNAs) are RNA molecules forming a closed loop, acting as microRNA sponges to regulate gene expression.
CircRNAs are increasingly recognized for their role in cancer pathology and potential as diagnostic biomarkers.
Existing databases require updates to incorporate comprehensive circRNA data and regulatory network information.

Purpose of the Study:

To present the updated CircNet database (version 2.0), enhancing its utility for circRNA research.
To integrate a large-scale dataset of circRNAs and their interactions from diverse sources.
To provide a robust, experimentally validated resource for studying circRNA-mediated gene regulation in cancer.

Main Methods:

Integrated circRNAs from circAtlas, MiOncoCirc, and The Cancer Genome Atlas (TCGA) into CircNet 2.0.
Analyzed 2732 cancer samples from 37 cancer types using advanced circRNA detection algorithms.
Predicted miRNA targets using PITA, miRanda, and TargetScan; incorporated 384,897 verified miRNA-target interactions from miRTarBase.

Main Results:

CircNet 2.0 houses an extensive collection of circRNAs across 37 cancer types.
Established high-quality circRNA-miRNA-gene regulatory networks based on predicted and validated interactions.
Developed a user-friendly web interface for data exploration, search, and visualization.

Conclusions:

The enhanced CircNet 2.0 database is a powerful, experimentally validated resource for biomedical research.
Provides strong data support for investigating circRNA functions and their roles in cancer.
Facilitates the discovery of novel cancer biomarkers and therapeutic targets through comprehensive network analysis.

Read full analysis

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