New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling
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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.
In: Plants, Vol. 10, No. 4, 646, 2021.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - New Cross-Talks between Pathways Involved in Grapevine Infection with ‘Candidatus Phytoplasma solani’ Revealed by Temporal Network Modelling
AU - Škrlj, Blaž
AU - Novak, Maruša Pompe
AU - Brader, Günter
AU - Anžič, Barbara
AU - Ramšak, Živa
AU - Gruden, Kristina
AU - Kralj, Jan
AU - Kladnik, Aleš
AU - Lavrač, Nada
AU - Roitsch, Thomas
AU - Dermastia, Marina
N1 - Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2021
Y1 - 2021
N2 - Understanding temporal biological phenomena is a challenging task that can be ap-proached 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 Phy-toplasma 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.
AB - Understanding temporal biological phenomena is a challenging task that can be ap-proached 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 Phy-toplasma 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.
KW - Bois noir
KW - Community detection
KW - Enrichment analysis
KW - Network analysis
KW - Phytoplasma
U2 - 10.3390/plants10040646
DO - 10.3390/plants10040646
M3 - Journal article
C2 - 33805409
AN - SCOPUS:85103092703
VL - 10
JO - Plants
JF - Plants
SN - 2223-7747
IS - 4
M1 - 646
ER -
ID: 262847461