Allergic diseases, such as asthma and hay fever, are not just simple allergies; they are complex conditions that can affect multiple organs and involve chronic inflammation. Researchers have been investigating the role of gene expression—how genes are turned on or off in response to various stimuli—in the development of these diseases. However, the scientific community has lacked a user-friendly platform to analyze and visualize the vast amount of gene expression data associated with allergic diseases.
What is CTPAD?
To address this gap, researchers at the Guangdong Academy of Medical Sciences have developed CTPAD, an interactive web tool designed to facilitate the analysis of gene expression data related to allergic diseases. Built using the Shiny framework, CTPAD allows researchers, even those without a background in bioinformatics, to easily explore and interpret transcriptomic data.
Workflow diagram presenting data collection, preprocessing, and web tool construction for the CTPAD web tool
How Does CTPAD Work?
CTPAD compiles gene expression profiles from both humans and mice, sourced from the Gene Expression Omnibus (GEO) database. By standardizing this data, the tool ensures that it can be easily compared and analyzed. Here are some of the key features of CTPAD:
Gene Expression Analysis: Users can examine how specific genes behave in allergic diseases, identifying patterns that may be linked to disease development.
Pathway Enrichment Analysis: This feature helps researchers understand which biological pathways are activated or suppressed in allergic diseases, providing insights into the underlying mechanisms.
Immune Infiltration Analysis: CTPAD estimates the proportions of various immune cells present in allergic conditions, shedding light on the immune system’s role in these diseases.
Correlation Analysis: Users can explore relationships between different genes and their expression levels, helping to uncover potential interactions.
Single-Cell RNA Sequencing Analysis: This advanced feature allows for a detailed examination of gene expression at the single-cell level, which is crucial for understanding the heterogeneity of allergic diseases.
User-Friendly Design
CTPAD is designed with accessibility in mind. The web application features customizable options for each analysis, enabling users to tailor the results to their specific research needs. Additionally, all output can be downloaded in PDF format with high-resolution images, making it easy for researchers to share their findings.
Why CTPAD is Important
By providing a comprehensive platform for the analysis of transcriptomic data, CTPAD empowers researchers from various fields to delve into the complexities of allergic diseases. It bridges the gap between advanced bioinformatics techniques and practical applications, ultimately aiming to enhance our understanding of how genetic factors contribute to these chronic conditions.
In summary, CTPAD is a significant step forward in the field of allergic disease research, facilitating more in-depth exploration of gene expression patterns and immune responses. This innovative tool promises to be an invaluable resource for researchers seeking to unravel the complexities of allergic diseases and improve treatment strategies.
Availability – CTPAD is available at https://smuonco.shinyapps.io/CTPAD/.