OncoDB: an Interactive Online Database for Analysis of Gene Expression and Viral Infection in Cancer

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2021 Oct 31

PMID 34718715

Citations 117

Authors

Gongyu Tang

Minsu Cho

Xiaowei Wang

Affiliations

Soon will be listed here.

Abstract

Large-scale multi-omics datasets, most prominently from the TCGA consortium, have been made available to the public for systematic characterization of human cancers. However, to date, there is a lack of corresponding online resources to utilize these valuable data to study gene expression dysregulation and viral infection, two major causes for cancer development and progression. To address these unmet needs, we established OncoDB, an online database resource to explore abnormal patterns in gene expression as well as viral infection that are correlated to clinical features in cancer. Specifically, OncoDB integrated RNA-seq, DNA methylation, and related clinical data from over 10 000 cancer patients in the TCGA study as well as from normal tissues in the GTEx study. Another unique aspect of OncoDB is its focus on oncoviruses. By mining TCGA RNA-seq data, we have identified six major oncoviruses across cancer types and further correlated viral infection to changes in host gene expression and clinical outcomes. All the analysis results are integratively presented in OncoDB with a flexible web interface to search for data related to RNA expression, DNA methylation, viral infection, and clinical features of the cancer patients. OncoDB is freely accessible at http://oncodb.org.

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