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...
Main Authors: | , , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Public Library of Science (PLoS)
2021-02-01
|
Series: | PLoS Computational Biology |
Online Access: | https://doi.org/10.1371/journal.pcbi.1008685 |
id |
doaj-00a6fe4655e94003bb64bc7e1cbd3785 |
---|---|
record_format |
Article |
spelling |
doaj-00a6fe4655e94003bb64bc7e1cbd37852021-04-21T16:41:04ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582021-02-01172e100868510.1371/journal.pcbi.1008685ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways.Agatha TreveilBalazs BoharPadhmanand SudhakarLejla GulLuca CsabaiMarton OlbeiMartina PolettiMatthew MadgwickTahila AndrighettiIsabelle HautefortDezso ModosTamas KorcsmarosThe 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.https://doi.org/10.1371/journal.pcbi.1008685 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Agatha Treveil Balazs Bohar Padhmanand Sudhakar Lejla Gul Luca Csabai Marton Olbei Martina Poletti Matthew Madgwick Tahila Andrighetti Isabelle Hautefort Dezso Modos Tamas Korcsmaros |
spellingShingle |
Agatha Treveil Balazs Bohar Padhmanand Sudhakar Lejla Gul Luca Csabai Marton Olbei Martina Poletti Matthew Madgwick Tahila Andrighetti Isabelle Hautefort Dezso Modos Tamas Korcsmaros ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PLoS Computational Biology |
author_facet |
Agatha Treveil Balazs Bohar Padhmanand Sudhakar Lejla Gul Luca Csabai Marton Olbei Martina Poletti Matthew Madgwick Tahila Andrighetti Isabelle Hautefort Dezso Modos Tamas Korcsmaros |
author_sort |
Agatha Treveil |
title |
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_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_sort |
virallink: an integrated workflow to investigate the effect of sars-cov-2 on intracellular signalling and regulatory pathways. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Computational Biology |
issn |
1553-734X 1553-7358 |
publishDate |
2021-02-01 |
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. |
url |
https://doi.org/10.1371/journal.pcbi.1008685 |
work_keys_str_mv |
AT agathatreveil virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT balazsbohar virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT padhmanandsudhakar virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT lejlagul virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT lucacsabai virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT martonolbei virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT martinapoletti virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT matthewmadgwick virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT tahilaandrighetti virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT isabellehautefort virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT dezsomodos virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways AT tamaskorcsmaros virallinkanintegratedworkflowtoinvestigatetheeffectofsarscov2onintracellularsignallingandregulatorypathways |
_version_ |
1714666683685142528 |