Preprint Article Version 2 This version is not peer-reviewed

Novel Method for Detection of Genes With Altered Expression Caused by Coronavirus Infection and Screening of Candidate Drugs for SARS-CoV-2

Version 1 : Received: 23 April 2020 / Approved: 24 April 2020 / Online: 24 April 2020 (09:21:20 CEST)
Version 2 : Received: 16 June 2020 / Approved: 17 June 2020 / Online: 17 June 2020 (13:26:51 CEST)

How to cite: Taguchi, Y.; Turki, T. Novel Method for Detection of Genes With Altered Expression Caused by Coronavirus Infection and Screening of Candidate Drugs for SARS-CoV-2. Preprints 2020, 2020040431 (doi: 10.20944/preprints202004.0431.v2). Taguchi, Y.; Turki, T. Novel Method for Detection of Genes With Altered Expression Caused by Coronavirus Infection and Screening of Candidate Drugs for SARS-CoV-2. Preprints 2020, 2020040431 (doi: 10.20944/preprints202004.0431.v2).

Abstract

To better understand the genes with altered expression caused by infection with the novel coronavirus strain SARS-CoV-2 causing COVID-19 infectious disease, a tensor decomposition (TD)-based unsupervised feature extraction (FE) approach was applied to a gene expression profile dataset of the mouse liver and spleen with experimental infection of mouse hepatitis virus, which is regarded as a suitable model of human coronavirus infection. TD-based unsupervised FE selected 134 altered genes, which were enriched in protein-protein interactions with orf1ab, polyprotein, and 3C-like protease that are well known to play critical roles in coronavirus infection, suggesting that these 134 genes can represent the coronavirus infectious process. We then selected compounds targeting the expression of the 134 selected genes based on a public domain database. The identified drug compounds were mainly related to known antiviral drugs, several of which were also included in those previously screened with an \textit{in silico} method to identify candidate drugs for treating COVID-19.

Subject Areas

COVID-19; SARS-CoV-2; in silico drug discovery; gene expression profile; tensor decomposition; feature extraction

Comments (1)

Comment 1
Received: 17 June 2020
Commenter: Y-H. Taguchi
Commenter's Conflict of Interests: Author
Comment: Revised based upon reviewers' comments.Two additional files of SARS-CoV infections to mouse lung are added.Comparision with SARS-CoV-2 proteins as well as drugs developed for SARS-CoV-2 were added.Several analysis using synthetic data is added
+ Respond to this comment

We encourage comments and feedback from a broad range of readers. See criteria for comments and our diversity statement.

Leave a public comment
Send a private comment to the author(s)
Views 0
Downloads 0
Comments 1
Metrics 0


×
Alerts
Notify me about updates to this article or when a peer-reviewed version is published.