Abstract
Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA’s complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform.
Highlights
Breast cancer is a high-risk heterogeneous disease [1, 2] and complicated biological features, which leads to various complex treatments and clinical outcomes [3]
The The Cancer Genome Atlas (TCGA) breast cancer database helps researchers accelerate the development of treatments and preventions for breast cancer [14], it could still be challenging for researchers
It is difficult for researchers to organize the TCGA data, especially for those who are unfamiliar with the structure of TCGA database or bioinformatics [16, 17]
Summary
Breast cancer is a high-risk heterogeneous disease [1, 2] and complicated biological features, which leads to various complex treatments and clinical outcomes [3]. Bcan.med.stu.edu.cn/) is proposed to provide several practical functions to users, like data customization, data visualization, and private data center, and so on It is an intuitive and high-efficient sharing platform. Users have the options to combine one or more downloaded tables from original TCGA platform and select several variables from each table to generate a new database based on their needs. By clicking “submit”, a new customized database including interested variables from interested tables is formed and saved in the private data center. In this procedure, sample sizes of the customized data with different barcodes will be automatically calculated by the terminal system.
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