CovidExpress

CovidExpress aggregates and analyzes approximately 1,500 human bulk RNA-seq datasets to characterize transcriptional responses to SARS-CoV-2 and related respiratory viruses.

Key Features:

• Dataset aggregation: Compiles ~1,500 human bulk RNA-seq datasets sourced from publicly available repositories.
• Biological scope: Covers transcriptional data from various tissues and cell lines under diverse experimental conditions, including SARS-CoV-2 and Rhinovirus infections.
• Differential gene expression analysis: Enables examination of differential expression patterns across biological contexts and experimental contrasts.
• Integrative analysis: Performs cross-dataset integration to identify commonly regulated genes and shared transcriptional signatures.
• Visualization of expression patterns: Provides computational visualizations to examine gene expression and differential expression results.
• Candidate gene discovery: Identifies specific commonly regulated genes such as OASL.
• Regulatory hypothesis generation: Highlights potential mechanisms such as a suggested FURIN positive feedback loop.

Scientific Applications:

• Transcriptional profiling: Investigating tissue- and cell-type-specific transcriptional responses to SARS-CoV-2 infection.
• Comparative virology: Comparing host responses between SARS-CoV-2 and other respiratory viruses such as Rhinovirus.
• Biomarker and target identification: Identifying differentially expressed and commonly regulated genes (e.g., OASL) as candidate biomarkers or therapeutic targets.
• Mechanistic hypothesis testing: Generating hypotheses about viral-host interaction mechanisms, including potential FURIN feedback loops.
• Support for translational research: Informing drug and vaccine development efforts through gene expression analyses.

Methodology:

Aggregates ~1,500 human bulk RNA-seq datasets from public repositories and performs integrative and differential gene expression analyses with expression-pattern visualizations.