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The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions

View ORCID ProfileL Perfetto, View ORCID ProfileC Pastrello, View ORCID ProfileN Del-Toro, View ORCID ProfileM Duesbury, M Iannuccelli, M Kotlyar, View ORCID ProfileL Licata, View ORCID ProfileB Meldal, K Panneerselvam, View ORCID ProfileS Panni, N Rahimzadeh, View ORCID ProfileS Ricard-Blum, L Salwinski, View ORCID ProfileA Shrivastava, View ORCID ProfileG Cesareni, View ORCID ProfileM Pellegrini, View ORCID ProfileS Orchard, View ORCID ProfileI Jurisica, View ORCID ProfileHH Hermjakob, View ORCID ProfileP Porras
doi: https://doi.org/10.1101/2020.06.16.153817
L Perfetto
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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C Pastrello
2Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
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N Del-Toro
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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M Duesbury
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
3UCLA-DOE Institute, UCLA, Los Angeles, USA
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M Iannuccelli
4Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
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M Kotlyar
2Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
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L Licata
4Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
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B Meldal
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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K Panneerselvam
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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S Panni
5Department of Biology, Ecology and Earth Sciences, Università della Calabria, Rende, Italy
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N Rahimzadeh
3UCLA-DOE Institute, UCLA, Los Angeles, USA
6Providence John Wayne Cancer Institute, Santa Monica, USA
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S Ricard-Blum
7Univ Lyon, University Claude Bernard Lyon 1, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne, France
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L Salwinski
3UCLA-DOE Institute, UCLA, Los Angeles, USA
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A Shrivastava
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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G Cesareni
4Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
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M Pellegrini
8Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, USA
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S Orchard
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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I Jurisica
2Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
9Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada
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HH Hermjakob
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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P Porras
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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  • For correspondence: pporras@ebi.ac.uk
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Abstract

The current Coronavirus Disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions enables studying fine-grained resolution of the mechanisms behind the virus biology and the human organism response. Here we present a curated dataset of physical molecular interactions, manually extracted by IMEx Consortium curators focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family. Currently, the dataset comprises over 2,200 binarized interactions extracted from 86 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (www.ebi.ac.uk/intact), and will be continuously updated as research on COVID-19 progresses.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • http://www.ebi.ac.uk/intact/resources/datasets

  • http://www.ndexbio.org/#/networkset/4c2268a1-a0f0-11ea-aaef-0ac135e8bacf

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 16, 2020.
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The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions
L Perfetto, C Pastrello, N Del-Toro, M Duesbury, M Iannuccelli, M Kotlyar, L Licata, B Meldal, K Panneerselvam, S Panni, N Rahimzadeh, S Ricard-Blum, L Salwinski, A Shrivastava, G Cesareni, M Pellegrini, S Orchard, I Jurisica, HH Hermjakob, P Porras
bioRxiv 2020.06.16.153817; doi: https://doi.org/10.1101/2020.06.16.153817
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The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions
L Perfetto, C Pastrello, N Del-Toro, M Duesbury, M Iannuccelli, M Kotlyar, L Licata, B Meldal, K Panneerselvam, S Panni, N Rahimzadeh, S Ricard-Blum, L Salwinski, A Shrivastava, G Cesareni, M Pellegrini, S Orchard, I Jurisica, HH Hermjakob, P Porras
bioRxiv 2020.06.16.153817; doi: https://doi.org/10.1101/2020.06.16.153817

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