CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes

Djekidel, M. N.; Rosikiewicz, W.; Peng, J. C.; Kanneganti, T.-D.; Hui, Y.; Jin, H.; Hedges, D.; Schreiner, P.; Fan, Y.; Wu, G.; Xu, B.

doi:10.1101/2021.05.14.444026

bioRxiv · 10.1101/2021.05.14.444026

CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes

Djekidel, M. N.·Rosikiewicz, W.·Peng, J. C.·Kanneganti, T.-D.·Hui, Y.·Jin, H.·Hedges, D.·Schreiner, P.·Fan, Y.·Wu, G.·Xu, B.

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Abstract

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans could cause coronavirus disease 2019 (COVID-19). Since its first discovery in Dec 2019, SARS-CoV-2 has become a global pandemic and caused 3.3 million direct/indirect deaths (2021 May). Amongst the scientific communitys response to COVID-19, data sharing has emerged as an essential aspect of the combat against SARS-CoV-2. Despite the ever-growing studies about SARS-CoV-2 and COVID-19, to date, only a few databases were curated to enable access to gene expression data. Furthermore, these databases curated only a small set of data and do not provide easy access for investigators without computational skills to perform analyses. To fill this gap and advance open-access to the growing gene expression data on this deadly virus, we collected about 1,500 human bulk RNA-seq datasets from publicly available resources, developed a database and visualization tool, named CovidExpress (https://stjudecab.github.io/covidexpress). This open access database will allow research investigators to examine the gene expression in various tissues, cell lines, and their response to SARS-CoV-2 under different experimental conditions, accelerating the understanding of the etiology of this disease to inform the drug and vaccine development. Our integrative analysis of this big dataset highlights a set of commonly regulated genes in SARS-CoV-2 infected lung and Rhinovirus infected nasal tissues, including OASL that were under-studied in COVID-19 related reports. Our results also suggested a potential FURIN positive feedback loop that might explain the evolutional advantage of SARS-CoV-2.

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Djekidel, M. N., Rosikiewicz, W., Peng, J. C., Kanneganti, T.-D., Hui, Y., Jin, H., Hedges, D., Schreiner, P., Fan, Y., Wu, G., Xu, B.. 2021-05-16. CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes. https://doi.org/10.1101/2021.05.14.444026

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