Abstract
BackgroundBrain cancer is one of the eight most common cancers occurring in people aged 40+ and is the fifth-leading cause of cancer-related deaths for males aged 40–59. Accurate subtype identification is crucial for precise therapeutic treatment, which largely depends on understanding the biological pathways and regulatory mechanisms associated with different brain cancer subtypes. Unfortunately, the subtype-implicated genes that have been identified are scattered in thousands of published studies. So, systematic literature curation and cross-validation could provide a solid base for comparative genetic studies about major subtypes.ResultsHere, we constructed a literature-based brain cancer gene database (BCGene). In the current release, we have a collection of 1421 unique human genes gathered through an extensive manual examination of over 6000 PubMed abstracts. We comprehensively annotated those curated genes to facilitate biological pathway identification, cancer genomic comparison, and differential expression analysis in various anatomical brain regions. By curating cancer subtypes from the literature, our database provides a basis for exploring the common and unique genetic mechanisms among 40 brain cancer subtypes. By further prioritizing the relative importance of those curated genes in the development of brain cancer, we identified 33 top-ranked genes with evidence mentioned only once in the literature, which were significantly associated with survival rates in a combined dataset of 2997 brain cancer cases.ConclusionBCGene provides a useful tool for exploring the genetic mechanisms of and gene priorities in brain cancer. BCGene is freely available to academic users at http://soft.bioinfo-minzhao.org/bcgene/.
Highlights
Brain cancer is one of the eight most common cancers occurring in people aged 40+ and is the fifthleading cause of cancer-related deaths for males aged 40–59
The literature frequency for various brain cancer subtypes Based on our comprehensive literature curation, we cleaned up all the associations between brain cancer genes and the literature before conducting further analyses
Astrocytoma, oligodendroglioma, ependymoma, GBM, low-grade glioma (LGG), ganglioglioma, and oligoastrocytoma were all grouped as gliomas, and medulloblastoma was grouped with neuroectodermal tumors
Summary
Brain cancer is one of the eight most common cancers occurring in people aged 40+ and is the fifthleading cause of cancer-related deaths for males aged 40–59. Accurate subtype identification is crucial for precise therapeutic treatment, which largely depends on understanding the biological pathways and regulatory mechanisms associated with different brain cancer subtypes. Systematic literature curation and crossvalidation could provide a solid base for comparative genetic studies about major subtypes. Glioma is the most common tumor type and includes astrocytoma, ependymoma, and oligodendroglioma. The overall 5-year survival rate of brain cancer patients is approximately 36%, but the 5-year survival rate of oligodendroglioma patients is about 80.6%, and the 10-year relative survival rate is 63.8%. Exact identification of glioma subtypes is essential for neuro-oncologists to provide the best treatment. Many existing clinical and histological methods identify brain cancer subtypes, molecular subtype information can independently and reliably confirm or refute those identifications, providing more accurate diagnostic evidence
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