Abstract
Gliomas are one of the most common types of brain cancers. Numerous efforts have been devoted to studying the mechanisms of glioma genesis and identifying biomarkers for diagnosis and treatment. To help further investigations, we present a comprehensive database named GliomaDB. GliomaDB includes 21,086 samples from 4303 patients and integrates genomic, transcriptomic, epigenomic, clinical, and gene-drug association data regarding glioblastoma multiforme (GBM) and low-grade glioma (LGG) from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), the Chinese Glioma Genome Atlas (CGGA), the Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT), the US Food and Drug Administration (FDA), and PharmGKB. GliomaDB offers a user-friendly interface for two main types of functionalities. The first comprises queries of (i) somatic mutations, (ii) gene expression, (iii) microRNA (miRNA) expression, and (iv) DNA methylation. In addition, queries can be executed at the gene, region, and base level. Second, GliomaDB allows users to perform survival analysis, coexpression network visualization, multi-omics data visualization, and targeted drug recommendations based on personalized variations. GliomaDB bridges the gap between glioma genomics big data and the delivery of integrated information for end users, thus enabling both researchers and clinicians to effectively use publicly available data and empowering the progression of precision medicine in glioma. GliomaDB is freely accessible at http://bigd.big.ac.cn/gliomaDB.
Highlights
Gliomas are the most common form of brain cancers and can be classified as Grade I–IV based on standards set by the World Health Organization (WHO)
Grade I, II, and III gliomas are usually considered low-grade glioma (LGG), whereas Grade IV tumors are frequently termed high-grade glioma, which is known as glioblastoma multiforme (GBM)
An enormous amount of data from independent studies has been deposited into Gene Expression Omnibus (GEO) [7,8]; both of these data aggregates provide an unprecedented opportunity for glioma research
Summary
Gliomas are the most common form of brain cancers and can be classified as Grade I–IV based on standards set by the World Health Organization (WHO). Some of the databases focus on pan-cancer expression analysis; for example, Gene Expression Profiling Interactive Analysis (GEPIA, http://gepia.cancer-pku.cn) [12] provides RNA sequencing (RNA-seq) data from 9736 tumors and 8587 normal samples from the TCGA and the Genotype-Tissue Expression (GTEx) projects and offers tools for differential analysis, similar gene analysis, correlation analysis, and dimensionality reduction. (2) GLIOMASdb (http://cgga.org.cn:9091/ gliomasdb/) [15] provides RNA-seq data of 325 gliomas at different stages with different subtypes and identified progression-associated genes.
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