omicscodeathon/ace2_covid

Expression Level Analysis of ACE2 Receptor Gene in COVID-19 Patients from African and Non-African Regions # Expression Level Analysis of ACE2 Receptor in African-American and non-African-American COVID-19 patients ## Global Malaria belt source: malariacampaign.gov.lk ## Background The global COVID-19 pandemic caused by SARS-CoV-2 has spread rapidly across the continents. While the incidence of COVID-19 has been reported to be higher among the African-American community, the rate of mortality has been lower compared to that of white and native Americans. ACE2 is involved in COVID-19 as SARS-CoV-2 uses the ACE2 enzyme to enter host cells. Although the difference in COVID-19 incidence can be explained by many factors such as low accesibility of health insuarance among Africa-American community, the variable expression of genes has been linked to this observed phenomenon. Little is known about ACE2 expression in African-American COVID-19 patients compared to non-African-American COVID-19 patients. ## General Objective To analyze expression level of ACE2 gene in African-American COVID-19 patients compared to non- African- American COVID-19 patients. ## Methods In this study, transcriptomes from African-American and non-African-American COVID-19 patients were downloaded from the NCBI sequence read archive (SRA) and analyzed for ACE2 gene expression. The reads were aligned to the human reference genome using HISAT2 and the raw counts generated using HTseq-count. EdgeR was used to conduct differential gene expression analysis with statistical analysis being done in R. ## Analysis Workflow ## Prerequisites for Analysis The data used for the analysis was retrieved from NCBI. The accession numbers for the data used can be found under accession. #### Tools and packages. Prior to installation of the analysis packages you need to have a unix environment i.e linux or macOS. Moreover you need to install R and RStudio IDE. ###### Installation of unix packages. ```bash #Fastqc v0.11.9 wget bioinformatics.babraham.ac.… …