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CTPAD: an interactive web application for comprehensive transcriptomic profiling in allergic diseases.

Suizi Zhou1,2, Wanqiao Huang3, Yitong Liu2

  • 1Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.

Journal of Translational Medicine
|October 14, 2024
PubMed
Summary
This summary is machine-generated.

Researchers can now explore allergic disease transcriptomic data using CTPAD, a new web tool. This platform simplifies complex gene expression analysis and visualization for a better understanding of allergic diseases.

Keywords:
Allergic diseasesBioinformaticsGeneTranscriptomic profilingVisualization

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Area of Science:

  • Biomedical research
  • Bioinformatics
  • Immunology

Background:

  • Allergic diseases are complex systemic inflammatory conditions with multiorgan damage.
  • Gene expression abnormalities are linked to allergic disease development.
  • A public platform for comprehensive transcriptomic data analysis in allergic diseases is lacking.

Purpose of the Study:

  • To develop a comprehensive web tool for multifaceted analysis of allergic diseases.
  • To provide researchers with an accessible platform for exploring transcriptomic data.

Main Methods:

  • Downloaded and standardized human and mouse gene expression data from the Gene Expression Omnibus (GEO) database.
  • Utilized MSigDB gene sets for pathway enrichment analysis and immune infiltration algorithms for immune cell proportion estimation.
  • Developed an interactive R Shiny web application with features like jQuery plugins and a user feedback system.

Main Results:

  • Developed CTPAD, an interactive R Shiny application for exploring allergic disease transcriptomic data.
  • Integrated public databases and multiple algorithms for gene expression, pathway enrichment, and immune infiltration analysis.
  • CTPAD offers customizable modules with high-resolution downloadable images.

Conclusions:

  • CTPAD significantly aids researchers, especially those without bioinformatics expertise, in exploring allergic disease transcriptomic features.
  • The tool enhances the understanding of the molecular underpinnings of allergic diseases.
  • CTPAD is publicly accessible at https://smuonco.shinyapps.io/CTPAD/.