OncoDB 2.0: a comprehensive platform for integrated pan-cancer omics analysis.

IF 13.1 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2025-09-23 DOI:10.1093/nar/gkaf952

Minsu Cho,Gongyu Tang,Charles S Rogers,Makayla Dove,Xinyi Liu,Yuanxiang Li,Xiaowei Wang

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引用次数: 0

Abstract

OncoDB was initially developed to advance cancer research by integrating RNA expression profiles, DNA methylation patterns, clinical annotations, and oncoviral signatures derived from the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression datasets. We now present OncoDB 2.0, an extensively expanded platform that offers a more comprehensive and integrated view of cancer omics. The updated version includes an atlas of somatic mutations discovered from combined DNA and RNA sequencing, enabling in-depth investigation of mutation patterns across tumor types and their association with clinical features. Furthermore, we have integrated proteomic data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and chromatin accessibility data from TCGA, offering new dimensions for oncogene regulation studies. OncoDB 2.0 also introduces advanced multi-omics analysis modules that facilitate the combined exploration of RNA expression, DNA methylation, and somatic mutations, allowing researchers to examine complex cross-omic relationships with greater depth and flexibility. Together, these enhancements make OncoDB 2.0 a robust and invaluable tool for the cancer research community. OncoDB 2.0 is freely available at https://oncodb.org.

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OncoDB 2.0：综合泛癌症组学分析的综合平台

OncoDB最初的开发目的是通过整合来自癌症基因组图谱（TCGA）和基因型组织表达数据集的RNA表达谱、DNA甲基化模式、临床注释和癌病毒特征来推进癌症研究。我们现在推出OncoDB 2.0，这是一个广泛扩展的平台，提供了更全面和集成的癌症组学视图。更新的版本包括从DNA和RNA组合测序中发现的体细胞突变图谱，能够深入研究肿瘤类型的突变模式及其与临床特征的关联。此外，我们整合了临床蛋白质组学肿瘤分析联盟（CPTAC）的蛋白质组学数据和TCGA的染色质可及性数据，为癌基因调控研究提供了新的维度。OncoDB 2.0还引入了先进的多组学分析模块，促进了RNA表达、DNA甲基化和体细胞突变的联合探索，使研究人员能够更深入、更灵活地研究复杂的跨组学关系。总之，这些增强功能使OncoDB 2.0成为癌症研究界一个强大而宝贵的工具。OncoDB 2.0可在https://oncodb.org免费获得。

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

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.