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COVID-19 in Patients: A Transcriptomic Profile

April 28, 2020

Of the few publications with published gene expression data from Covid-19 patients, a recent manuscript in ‘Emerging Microbes and Infections’ investigated the transcriptomic host response to infection of SARS-CoV-2. In order to give more color to the findings, we analyzed the published gene expression data on our software and are pleased to share our analyses here.


At PercayAI, we want to share transparent analyses with the scientific community in order to help uncover novel hypotheses to target Covid-19. We are therefore using our AI tools to help colleagues worldwide gain a better collective understanding of the virus and potential treatments. If you have COVID-19 data you'd like us to analyze using our tool, free of charge, reach out to get in touch with our team.


In the study cited above, the authors profiled the respiratory response through bronchoalveolar lavage fluid (BALF) samples and the systemic response through peripheral blood mononuclear cells (PBMC) samples from COVID-19 patients compared to healthy controls. The authors observed an increase in cell death and an exaggerated inflammatory cytokine response induced by SARS-CoV-2, which may lead to lymphopenia. 


This initial post will examine the BALF sample analysis that we completed with the aid of our AI tool. Read part 2 for the analysis of the systemic response through peripheral blood mononuclear cells (PBMC) samples.

COVID-19 in Patient Respiratory System

We analyzed up- and down-regulated genes derived from BALF samples and identified processes that are enhanced or impeded by the infection.

Upregulated Host Response to COVID-19
PercayAI - COVID-19 in Patient Respirato

General Overview: 

  • In purple (middle top) are markers of epithelial cells. 

  • In teal (center) are barrier and structural mechanisms.

  • In orange (middle lower) are markers of ciliated cells. 

  • In red-pink (right bottom) are nutrient and metabolism processes. 

  • In light pink (left top) are mucosal associated processes. 

  • In light purple (left bottom), basic cellular functions are represented. 

  • In blue (top right) are circulating factors that suggest damage to blood cells.

  • In green (middle) are developmental factors associated with early differentiation. 


Key Takeaways: 

  • Multiple signatures suggest an increased effort to enhance the barrier within the respiratory system via mucosal and epithelial cells and related processes. This may be a compensatory, protective response to the virus.

  • Interestingly, even within the respiratory system, we detect the damaged blood cell signature noted by the authors.

  • The nutrient metabolic signature may suggest that cells are dying in response to the viral attack.

Downregulated Host Response to COVID-19
PercayAI - COVID-19 in Patient Respirato

General Overview: 

  • In purple (left bottom) are trafficking and lysosome processes. 

  • In red-pink (right bottom) are immune and antiviral responses. 

  • In blue (top middle) are several metabolic processes.

  • In green (middle) are various intracellular signaling processes. 


Key Takeaways: 

  • The down-regulation of immune responses suggests an impairment in defensive mechanisms. Specifically, Interferon signaling, a key pathway in viral-mediated responses may be impeded by SARS-CoV-2.

  • Diminished lysosomal functions may be be enabling infection. 

  • Together, these down-regulated processes may offer insights into discovering therapeutic targets in order to improve outcomes against Covid-19.

In conclusion, our AI tool allowed us to quickly convert available research findings into an easy-to-understand visualization, which helped our computational biologists make connections of their own. The ability for researchers to become well-versed in the current literature and identify scientifically grounded, testable hypotheses in a timely manner will accelerate the timeline to effective drug treatments.


Leave a comment below with your impressions, or send us a message here. If you have COVID-19 data you'd like us to run, free of charge, reach out here, so our team can contact you with potential next steps.

Read part 2 for the analysis of the systemic response through peripheral blood mononuclear cells (PBMC) samples.

Share your impressions

Send us an idea or share your feedback below. We may test it in CompBio, and create and share hypotheses on the blog.*

*We are launching this webpage to share knowledge maps of Coronavirus and to encourage hypotheses generation. We invite you to share your ideas, insights, and feedback (“Feedback”) to help us create hypotheses in connection with Coronavirus therapies, treatments, and solutions. Please click on the links below which cover our Right to Use Feedback, and important Disclaimers. By submitting Feedback, you agree that you have read and agree to these terms. Thank you for your participation in this project.


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