C2CDB: an advanced platform integrating comprehensive information and analysis tools of cancer-related circRNAs.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2024-08-16 eCollection Date: 2024-01-01 DOI:10.1093/bioadv/vbae112

Yuanli Zuo, Wenrong Liu, Yang Jin, Yitong Pan, Ting Fan, Xin Fu, Jiawei Guo, Shuangyan Tan, Juan He, Yang Yang, Zhang Li, Chenyu Yang, Yong Peng

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引用次数: 0

Abstract

Motivation: Circular RNAs (circRNAs) play important roles in gene expression and their involvement in tumorigenesis is emerging. circRNA-related database is a powerful tool for researchers to investigate circRNAs. However, existing databases lack advanced platform integrating comprehensive information and analysis tools of cancer-related circRNAs.

Results: We developed a comprehensive platform called CircRNA to Cancer Database (C2CDB), encompassing 318 158 cancer-related circRNAs expressed in tumors and adjacent tissues across 30 types of cancers. C2CDB provides basic details such as sequence and expression levels of circRNAs, as well as crucial insights into biological mechanisms, including miRNA binding, RNA-binding protein interaction, coding potential, base modification, mutation, and secondary structure. Moreover, C2CDB collects an extensive compilation of published literature on cancer circRNAs, extracting and presenting pivotal content encompassing biological functions, underlying mechanisms, and molecular tools in these studies. Additionally, C2CDB offers integrated tools to analyse three potential mechanisms: circRNA-miRNA ceRNA interaction, circRNA encoding, and circRNA biogenesis, facilitating investigators with convenient access to highly reliable information. To enhance clarity and organization, C2CDB has meticulously curated and integrated the previously chaotic nomenclature of circRNAs, addressing the prevailing confusion and ambiguity surrounding their designations.

Availability and implementation: C2CDB is freely available at http://pengyonglab.com/c2cdb.

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C2CDB：一个集成了癌症相关 circRNAs 综合信息和分析工具的先进平台。

动因：环状RNA（circRNA）在基因表达中发挥着重要作用，其参与肿瘤发生的情况正在逐渐显现。环状RNA相关数据库是研究人员研究环状RNA的有力工具。然而，现有数据库缺乏整合癌症相关 circRNAs 综合信息和分析工具的先进平台：我们开发了一个名为 "癌症循环RNA数据库（CircRNA to Cancer Database，C2CDB）"的综合平台，涵盖了30种癌症中318 158个在肿瘤和邻近组织中表达的癌症相关循环RNA。C2CDB提供了circRNA的序列和表达水平等基本信息，以及对生物学机制的重要见解，包括miRNA结合、RNA结合蛋白相互作用、编码潜能、碱基修饰、突变和二级结构等。此外，C2CDB 收集了大量已发表的癌症 circRNAs 文献，提取并呈现了这些研究中涵盖生物功能、基本机制和分子工具的关键内容。此外，C2CDB 还提供了综合工具，用于分析 circRNA-miRNA ceRNA 相互作用、circRNA 编码和 circRNA 生物发生这三种潜在机制，方便研究人员获取高度可靠的信息。为了提高清晰度和组织性，C2CDB 对以前混乱的 circRNA 命名方法进行了精心整理和整合，解决了目前围绕其命名的混乱和模糊问题：C2CDB 可从 http://pengyonglab.com/c2cdb 免费获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Bioinformatics advances

CiteScore

1.60

自引率

0.00%

发文量