HPAanalyze：一个 R 包，可方便地检索和分析 Human Protein Atlas 数据。
HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data.
机构信息
Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, THT 948, 1900 University Blvd, Birmingham, AL, 35294, USA.
Department of Pathology, University of Alabama at Birmingham, 121 Shelby Biomedical Research Building, Birmingham, AL, 35294, USA.
出版信息
BMC Bioinformatics. 2019 Sep 9;20(1):463. doi: 10.1186/s12859-019-3059-z.
BACKGROUND
The Human Protein Atlas (HPA) aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics. Access of the HPA data is mainly via web-based interface allowing views of individual proteins, which may not be optimal for data analysis of a gene set, or automatic retrieval of original images.
RESULTS
HPAanalyze is an R package for retrieving and performing exploratory analysis of data from HPA. HPAanalyze provides functionality for importing data tables and xml files from HPA, exporting and visualizing data, as well as downloading all staining images of interest. The package is free, open source, and available via Bioconductor and GitHub. We provide examples of the use of HPAanalyze to investigate proteins altered in the deadly brain tumor glioblastoma. For example, we confirm Epidermal Growth Factor Receptor elevation and Phosphatase and Tensin Homolog loss and suggest the importance of the GTP Cyclohydrolase I/Tetrahydrobiopterin pathway. Additionally, we provide an interactive website for non-programmers to explore and visualize data without the use of R.
CONCLUSIONS
HPAanalyze integrates into the R workflow with the tidyverse framework, and it can be used in combination with Bioconductor packages for easy analysis of HPA data.
背景
人类蛋白质图谱（HPA）旨在通过包括成像、蛋白质组学和转录组学在内的多种技术来绘制人类蛋白质图谱。HPA 数据的访问主要通过基于网络的界面进行，允许查看单个蛋白质，这对于基因集的数据分析或原始图像的自动检索可能不是最佳选择。
结果
HPAanalyze 是一个用于从 HPA 检索和执行数据探索性分析的 R 包。HPAanalyze 提供了从 HPA 导入数据表和 xml 文件、导出和可视化数据以及下载所有感兴趣的染色图像的功能。该软件包是免费的、开源的，可以通过 Bioconductor 和 GitHub 使用。我们提供了使用 HPAanalyze 来研究致命脑肿瘤胶质母细胞瘤中改变的蛋白质的示例。例如，我们确认表皮生长因子受体（Epidermal Growth Factor Receptor）升高和磷酸酶和张力蛋白同源物（Phosphatase and Tensin Homolog）丢失，并表明 GTP 环化水解酶 I/四氢生物蝶呤途径的重要性。此外，我们还提供了一个非程序员的交互式网站，用于无需使用 R 即可探索和可视化数据。
结论
HPAanalyze 与 tidyverse 框架集成到 R 工作流程中，可以与 Bioconductor 包结合使用，以便轻松分析 HPA 数据。
Zotero 插件