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New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling

Understanding temporal biological phenomena is a challenging task that can be approached using network analysis. Here, we explored whether network reconstruction can be used to better understand the temporal dynamics of bois noir, which is associated with ‘Candidatus Phytoplasma solani’, and is one...

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Autores principales: Škrlj, Blaž, Novak, Maruša Pompe, Brader, Günter, Anžič, Barbara, Ramšak, Živa, Gruden, Kristina, Kralj, Jan, Kladnik, Aleš, Lavrač, Nada, Roitsch, Thomas, Dermastia, Marina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8065506/
https://www.ncbi.nlm.nih.gov/pubmed/33805409
http://dx.doi.org/10.3390/plants10040646
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author Škrlj, Blaž
Novak, Maruša Pompe
Brader, Günter
Anžič, Barbara
Ramšak, Živa
Gruden, Kristina
Kralj, Jan
Kladnik, Aleš
Lavrač, Nada
Roitsch, Thomas
Dermastia, Marina
author_facet Škrlj, Blaž
Novak, Maruša Pompe
Brader, Günter
Anžič, Barbara
Ramšak, Živa
Gruden, Kristina
Kralj, Jan
Kladnik, Aleš
Lavrač, Nada
Roitsch, Thomas
Dermastia, Marina
author_sort Škrlj, Blaž
collection PubMed
description Understanding temporal biological phenomena is a challenging task that can be approached using network analysis. Here, we explored whether network reconstruction can be used to better understand the temporal dynamics of bois noir, which is associated with ‘Candidatus Phytoplasma solani’, and is one of the most widespread phytoplasma diseases of grapevine in Europe. We proposed a methodology that explores the temporal network dynamics at the community level, i.e., densely connected subnetworks. The methodology offers both insights into the functional dynamics via enrichment analysis at the community level, and analyses of the community dissipation, as a measure that accounts for community degradation. We validated this methodology with cases on experimental temporal expression data of uninfected grapevines and grapevines infected with ‘Ca. P. solani’. These data confirm some known gene communities involved in this infection. They also reveal several new gene communities and their potential regulatory networks that have not been linked to ‘Ca. P. solani’ to date. To confirm the capabilities of the proposed method, selected predictions were empirically evaluated.
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spelling pubmed-80655062021-04-25 New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling Škrlj, Blaž Novak, Maruša Pompe Brader, Günter Anžič, Barbara Ramšak, Živa Gruden, Kristina Kralj, Jan Kladnik, Aleš Lavrač, Nada Roitsch, Thomas Dermastia, Marina Plants (Basel) Article Understanding temporal biological phenomena is a challenging task that can be approached using network analysis. Here, we explored whether network reconstruction can be used to better understand the temporal dynamics of bois noir, which is associated with ‘Candidatus Phytoplasma solani’, and is one of the most widespread phytoplasma diseases of grapevine in Europe. We proposed a methodology that explores the temporal network dynamics at the community level, i.e., densely connected subnetworks. The methodology offers both insights into the functional dynamics via enrichment analysis at the community level, and analyses of the community dissipation, as a measure that accounts for community degradation. We validated this methodology with cases on experimental temporal expression data of uninfected grapevines and grapevines infected with ‘Ca. P. solani’. These data confirm some known gene communities involved in this infection. They also reveal several new gene communities and their potential regulatory networks that have not been linked to ‘Ca. P. solani’ to date. To confirm the capabilities of the proposed method, selected predictions were empirically evaluated. MDPI 2021-03-29 /pmc/articles/PMC8065506/ /pubmed/33805409 http://dx.doi.org/10.3390/plants10040646 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Škrlj, Blaž
Novak, Maruša Pompe
Brader, Günter
Anžič, Barbara
Ramšak, Živa
Gruden, Kristina
Kralj, Jan
Kladnik, Aleš
Lavrač, Nada
Roitsch, Thomas
Dermastia, Marina
New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling
title New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling
title_full New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling
title_fullStr New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling
title_full_unstemmed New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling
title_short New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling
title_sort new cross-talks between pathways involved in grapevine infection with ‘candidatus phytoplasma solani’ revealed by temporal network modelling
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8065506/
https://www.ncbi.nlm.nih.gov/pubmed/33805409
http://dx.doi.org/10.3390/plants10040646
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