Celiku Orieta, Johnson Seth, Zhao Shuping, Camphausen Kevin, Shankavaram Uma
Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
PLoS One. 2014 Jul 10;9(7):e101239. doi: 10.1371/journal.pone.0101239. eCollection 2014.
Validation of clinical biomarkers and response to therapy is a challenging topic in cancer research. An important source of information for virtual validation is the datasets generated from multi-center cancer research projects such as The Cancer Genome Atlas project (TCGA). These data enable investigation of genetic and epigenetic changes responsible for cancer onset and progression, response to cancer therapies, and discovery of the molecular profiles of various cancers. However, these analyses often require bulk download of data and substantial bioinformatics expertise, which can be intimidating for investigators. Here, we report on the development of a new resource available to scientists: a data base called Glioblastoma Bio Discovery Portal (GBM-BioDP). GBM-BioDP is a free web-accessible resource that hosts a subset of the glioblastoma TCGA data and enables an intuitive query and interactive display of the resultant data. This resource provides visualization tools for the exploration of gene, miRNA, and protein expression, differential expression within the subtypes of GBM, and potential associations with clinical outcome, which are useful for virtual biological validation. The tool may also enable generation of hypotheses on how therapies impact GBM molecular profiles, which can help in personalization of treatment for optimal outcome. The resource can be accessed freely at http://gbm-biodp.nci.nih.gov (a tutorial is included).
临床生物标志物的验证及对治疗的反应是癌症研究中一个具有挑战性的课题。虚拟验证的一个重要信息来源是多中心癌症研究项目（如癌症基因组图谱计划，即TCGA）所产生的数据集。这些数据有助于研究导致癌症发生和进展的遗传和表观遗传变化、对癌症治疗的反应以及发现各种癌症的分子特征。然而，这些分析通常需要大量下载数据并具备丰富的生物信息学专业知识，这可能会让研究人员望而却步。在此，我们报告一种可供科学家使用的新资源的开发情况：一个名为胶质母细胞瘤生物发现门户（GBM - BioDP）的数据库。GBM - BioDP是一个可通过网络免费访问的资源，它存储了胶质母细胞瘤TCGA数据的一个子集，并能对所得数据进行直观查询和交互式展示。该资源提供了可视化工具，用于探索基因、miRNA和蛋白质表达、GBM各亚型内的差异表达以及与临床结果的潜在关联，这对虚拟生物学验证很有用。该工具还可能有助于生成关于治疗如何影响GBM分子特征的假设，这有助于实现个性化治疗以获得最佳疗效。可通过http://gbm-biodp.nci.nih.gov免费访问该资源（其中包含一个教程）。
