chr991004/covid-19_severity

COVID-19 disease severity related gene screening and analysis.

COVID-19 Severity-Related Gene Expression Analysis

This repository contains the R scripts and data files used in the study "Leveraging RNA-seq Data to Understand the Molecular Mechanisms Associated with Varying Levels of COVID-19 Severity". The research identifies dynamic gene expression patterns correlated with disease progression using both bulk RNA-seq and single-cell RNA-seq (scRNA-seq) data from COVID-19 patients and healthy individuals.

Repository Structure

The repository is organized as follows:

• Identification and visualization of gene expression patterns.R: This R script is used to identify and visualize the gene expression patterns associated with COVID-19 severity based on RNA-seq data. Four distinct expression trends have been identified.

• Gene_enrichment.R: This R script is used to conduct pathway enrichment analyses on the genes of interest. The analysis revealed a range of impacted pathways, from immune response to circadian rhythm.

• scRNA-seq analysis.R: This R script is used to perform in-depth single-cell analysis. The results provide further insights into the heterogeneity and specific cellular localization of the different expression patterns.

• model_gene_plot.pdf: This is the output visualization of the gene expression model, showing the distinct gene expression trends associated with COVID-19 severity.

• Required files: This folder contains necessary data files for the scripts:

  • all_results.Rdata: This file stores the results from the analyses.
  • GSE152418_filtered_metadata.csv: This file contains the filtered metadata for the GSE152418 dataset used in the analyses.
  • GSE152418_GeneLevel_Raw_data.csv: This file contains the raw gene-level data for the GSE152418 dataset.

Usage

To reproduce the analyses, first, clone this repository. Make sure you have the latest version of R and necessary R packages installed. Then, simply run the R scripts in the order provided above. Note that you might need to set your working directory to the location where the scripts are saved.

Related Resources

All findings have been consolidated in the COVID-19 Severity Related Database (http://covid.haoran.pub/), a web-based platform that aims to facilitate further research and potential therapeutic developments.

Contact

For any questions or concerns, please open an issue in this repository, or contact the maintainers directly.

Acknowledgments

We would like to thank all those who have contributed to this project, and the brave individuals who participated in the studies that provided the data for our analyses.