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ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways
The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralL...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7886129/ https://www.ncbi.nlm.nih.gov/pubmed/33534793 http://dx.doi.org/10.1371/journal.pcbi.1008685 |
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author | Treveil, Agatha Bohar, Balazs Sudhakar, Padhmanand Gul, Lejla Csabai, Luca Olbei, Marton Poletti, Martina Madgwick, Matthew Andrighetti, Tahila Hautefort, Isabelle Modos, Dezso Korcsmaros, Tamas |
author_facet | Treveil, Agatha Bohar, Balazs Sudhakar, Padhmanand Gul, Lejla Csabai, Luca Olbei, Marton Poletti, Martina Madgwick, Matthew Andrighetti, Tahila Hautefort, Isabelle Modos, Dezso Korcsmaros, Tamas |
author_sort | Treveil, Agatha |
collection | PubMed |
description | The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs and analyses networks representing the effect of viruses on intracellular signalling. These networks trace the flow of signal from intracellular viral proteins through their human binding proteins and downstream signalling pathways, ending with transcription factors regulating genes differentially expressed upon viral exposure. In this way, the workflow provides a mechanistic insight from previously identified knowledge of virally infected cells. By default, the workflow is set up to analyse the intracellular effects of SARS-CoV-2, requiring only transcriptomics counts data as input from the user: thus, encouraging and enabling rapid multidisciplinary research. However, the wide-ranging applicability and modularity of the workflow facilitates customisation of viral context, a priori interactions and analysis methods. Through a case study of SARS-CoV-2 infected bronchial/tracheal epithelial cells, we evidence the functionality of the workflow and its ability to identify key pathways and proteins in the cellular response to infection. The application of ViralLink to different viral infections in a context specific manner using different available transcriptomics datasets will uncover key mechanisms in viral pathogenesis. |
format | Online Article Text |
id | pubmed-7886129 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-78861292021-02-23 ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways Treveil, Agatha Bohar, Balazs Sudhakar, Padhmanand Gul, Lejla Csabai, Luca Olbei, Marton Poletti, Martina Madgwick, Matthew Andrighetti, Tahila Hautefort, Isabelle Modos, Dezso Korcsmaros, Tamas PLoS Comput Biol Research Article The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs and analyses networks representing the effect of viruses on intracellular signalling. These networks trace the flow of signal from intracellular viral proteins through their human binding proteins and downstream signalling pathways, ending with transcription factors regulating genes differentially expressed upon viral exposure. In this way, the workflow provides a mechanistic insight from previously identified knowledge of virally infected cells. By default, the workflow is set up to analyse the intracellular effects of SARS-CoV-2, requiring only transcriptomics counts data as input from the user: thus, encouraging and enabling rapid multidisciplinary research. However, the wide-ranging applicability and modularity of the workflow facilitates customisation of viral context, a priori interactions and analysis methods. Through a case study of SARS-CoV-2 infected bronchial/tracheal epithelial cells, we evidence the functionality of the workflow and its ability to identify key pathways and proteins in the cellular response to infection. The application of ViralLink to different viral infections in a context specific manner using different available transcriptomics datasets will uncover key mechanisms in viral pathogenesis. Public Library of Science 2021-02-03 /pmc/articles/PMC7886129/ /pubmed/33534793 http://dx.doi.org/10.1371/journal.pcbi.1008685 Text en © 2021 Treveil et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Treveil, Agatha Bohar, Balazs Sudhakar, Padhmanand Gul, Lejla Csabai, Luca Olbei, Marton Poletti, Martina Madgwick, Matthew Andrighetti, Tahila Hautefort, Isabelle Modos, Dezso Korcsmaros, Tamas ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways |
title | ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways |
title_full | ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways |
title_fullStr | ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways |
title_full_unstemmed | ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways |
title_short | ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways |
title_sort | virallink: an integrated workflow to investigate the effect of sars-cov-2 on intracellular signalling and regulatory pathways |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7886129/ https://www.ncbi.nlm.nih.gov/pubmed/33534793 http://dx.doi.org/10.1371/journal.pcbi.1008685 |
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