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The COVID-19 Gene and Drug Set Library

23 Pages Posted: 27 May 2020 Publication Status: Published

See all articles by Maxim Kuleshov

Maxim Kuleshov

Mount Sinai Health System - Department of Pharmacological Sciences

Daniel J. B. Clarke

Mount Sinai Health System - Department of Pharmacological Sciences

Eryk Kropiwnicki

Mount Sinai Health System - Department of Pharmacological Sciences

Kathleen Jagodnik

Mount Sinai Health System - Department of Pharmacological Sciences

Alon Bartal

Mount Sinai Health System - Department of Pharmacological Sciences

John Erol Evangelista

Mount Sinai Health System - Department of Pharmacological Sciences

Abigail Zhou

Mount Sinai Health System - Department of Pharmacological Sciences

Laura B. Ferguson

University of Texas at Austin - Department of Neurology

Alexander Lachmann

Mount Sinai Health System - Department of Pharmacological Sciences

Avi Ma'ayan

Icahn School of Medicine at Mount Sinai - Department of Pharmacological Sciences

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Abstract

The coronavirus (CoV) severe acute respiratory syndrome (SARS)-CoV-2 (COVID-19) pandemic has received rapid response by the research community to offer suggestions for repurposing of approved drugs as well as to improve our understanding of the COVID-19 viral life cycle molecular mechanisms. In a short period, tens of thousands of research preprints and other publications have emerged including those that report lists of experimentally validated drugs and compounds as potential COVID-19 therapies. In addition, gene sets from interacting COVID-19 virus-host proteins and differentially expressed genes when comparing infected to uninfected cells are being published at a fast rate. To organize this rapidly accumulating knowledge, we developed the COVID-19 Gene and Drug Set Library (https://amp.pharm.mssm.edu/covid19/), a collection of gene and drug sets related to COVID-19 research from multiple sources. The COVID-19 Gene and Drug Set Library is delivered as a web-based interface that enables users to view, download, analyze, visualize, and contribute gene and drug sets related to COVID-19 research. To evaluate the content of the library, we performed several analyses including comparing the results from 6 in-vitro drug screens for COVID-19 repurposing candidates. Surprisingly, we observe little overlap across these initial screens. The most common and unique hit across these screen is mefloquine, a malaria drug that should receive more attention as a potential therapeutic for COVID-19. Overall, the library of gene and drug sets can be used to identify community consensus, make researchers and clinicians aware of the development of new potential therapies, as well as allow the research community to work together towards a cure for COVID-19.

Funding: This project is partially funded by U54HL127624 and U24CA224260.

Keywords: SARS-COV-2, COVID-19, Gene Set Enrichment Analysis, Drug set Enrichment Analysis, Venn Diagrams, Drug Screens, Twitter Mining

Suggested Citation

Kuleshov, Maxim and Clarke, Daniel J. B. and Kropiwnicki, Eryk and Jagodnik, Kathleen and Bartal, Alon and Evangelista, John Erol and Zhou, Abigail and Ferguson, Laura B. and Lachmann, Alexander and Ma'ayan, Avi, The COVID-19 Gene and Drug Set Library. Available at SSRN: https://ssrn.com/abstract=3606799 or http://dx.doi.org/10.2139/ssrn.3606799
This version of the paper has not been formally peer reviewed.

Maxim Kuleshov

Mount Sinai Health System - Department of Pharmacological Sciences ( email )

One Gustave L. Levy Place
New York, NY 10029-6574
United States

Daniel J. B. Clarke

Mount Sinai Health System - Department of Pharmacological Sciences

One Gustave L. Levy Place
New York, NY 10029-6574
United States

Eryk Kropiwnicki

Mount Sinai Health System - Department of Pharmacological Sciences ( email )

One Gustave L. Levy Place
New York, NY 10029-6574
United States

Kathleen Jagodnik

Mount Sinai Health System - Department of Pharmacological Sciences ( email )

One Gustave L. Levy Place
New York, NY 10029-6574
United States

Alon Bartal

Mount Sinai Health System - Department of Pharmacological Sciences ( email )

One Gustave L. Levy Place
New York, NY 10029-6574
United States

John Erol Evangelista

Mount Sinai Health System - Department of Pharmacological Sciences ( email )

One Gustave L. Levy Place
New York, NY 10029-6574
United States

Abigail Zhou

Mount Sinai Health System - Department of Pharmacological Sciences ( email )

One Gustave L. Levy Place
New York, NY 10029-6574
United States

Laura B. Ferguson

University of Texas at Austin - Department of Neurology

Austin, TX 78712

Alexander Lachmann

Mount Sinai Health System - Department of Pharmacological Sciences

United States

Avi Ma'ayan (Contact Author)

Icahn School of Medicine at Mount Sinai - Department of Pharmacological Sciences ( email )

New, NY
United States

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