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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...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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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. |
format | Online Article Text |
id | pubmed-8065506 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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