Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
Department of Otolaryngology-Head and Neck Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510000, Guangdong, China.
J Transl Med. 2024 Oct 14;22(1):935. doi: 10.1186/s12967-024-05459-2.
Allergic diseases are systemic chronic inflammatory diseases associated with multiorgan damage and complex pathogenesis. Several studies have revealed the association of gene expression abnormalities with the development of allergic diseases, but the biomedical field still lacks a public platform for comprehensive analysis and visualization of transcriptomic data of allergic diseases.
The aim of the study is to provide a comprehensive web tool for multiple analysis in allergic diseases.
We retrieved and downloaded human and mouse gene expression profile data associated with allergic diseases from the Gene Expression Omnibus (GEO) database and standardized the data uniformly. We used gene sets obtained from the MSigDB database for pathway enrichment analysis and multiple immune infiltration algorithms for the estimation of immune cell proportion. The basic construction of the web pages was based on the Shiny framework. Additionally, more convenient features were added to the server to improve the efficiency of the web pages, such as jQuery plugins and a comment box to collect user feedback.
We developed CTPAD, an interactive R Shiny application that integrates public databases and multiple algorithms to explore allergic disease-related datasets and implement rich transcriptomic visualization capabilities, including gene expression analysis, pathway enrichment analysis, immune infiltration analysis, correlation analysis, and single-cell RNA sequencing analysis. All functional modules offer customization options and can be downloaded in PDF format with high-resolution images.
CTPAD largely facilitates the work of researchers without bioinformatics background to enable them to better explore the transcriptomic features associated with allergic diseases. CTPAD is available at https://smuonco.shinyapps.io/CTPAD/ .
过敏性疾病是全身性慢性炎症性疾病，与多器官损伤和复杂发病机制有关。多项研究表明，基因表达异常与过敏性疾病的发生有关，但生物医学领域仍缺乏一个用于综合分析和可视化过敏性疾病转录组数据的公共平台。
本研究旨在提供一个用于过敏性疾病多方面分析的综合网络工具。
我们从基因表达综合数据库（GEO）中检索并下载了与过敏性疾病相关的人类和小鼠基因表达谱数据，并对数据进行了统一标准化。我们使用从 MSigDB 数据库获得的基因集进行通路富集分析，并采用多种免疫浸润算法估计免疫细胞比例。网页的基本结构基于 Shiny 框架。此外，我们还在服务器上添加了更方便的功能，如 jQuery 插件和评论框，以收集用户反馈，从而提高网页的效率。
我们开发了 CTPAD，这是一个交互式的 R Shiny 应用程序，它集成了公共数据库和多种算法，用于探索与过敏性疾病相关的数据集，并实现了丰富的转录组可视化功能，包括基因表达分析、通路富集分析、免疫浸润分析、相关性分析和单细胞 RNA 测序分析。所有功能模块都提供了自定义选项，并可以以高分辨率图像的 PDF 格式下载。
CTPAD 极大地方便了没有生物信息学背景的研究人员的工作，使他们能够更好地探索与过敏性疾病相关的转录组特征。CTPAD 可在 https://smuonco.shinyapps.io/CTPAD/ 上获取。
