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New cross-talks between pathways involved in grapevine infection with ʼCandidatus Phytoplasma solaniʼ revealed by temporal network modelling
ID
Škrlj, Blaž
(
Author
),
ID
Pompe Novak, Maruša
(
Author
),
ID
Brader, Günter
(
Author
),
ID
Anžič, Barbara
(
Author
),
ID
Ramšak, Živa
(
Author
),
ID
Gruden, Kristina
(
Author
),
ID
Kralj, Jan
(
Author
),
ID
Kladnik, Aleš
(
Author
),
ID
Lavrač, Nada
(
Author
),
ID
Roitsch, Thomas
(
Author
),
ID
Dermastia, Marina
(
Author
)
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MD5: 8E524196E08CE4930624916719FF4649
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https://www.mdpi.com/2223-7747/10/4/646
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Abstract
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.
Language:
English
Keywords:
community detection
,
enrichment analysis
,
network analysis
,
phytoplasma
,
bois noir
Work type:
Article
Typology:
1.01 - Original Scientific Article
Organization:
BF - Biotechnical Faculty
Publication status:
Published
Publication version:
Version of Record
Year:
2021
Number of pages:
18 str.
Numbering:
Vol. 10, iss. 4, art. 646
PID:
20.500.12556/RUL-135237
UDC:
577
ISSN on article:
2223-7747
DOI:
10.3390/plants10040646
COBISS.SI-ID:
58899971
Publication date in RUL:
02.03.2022
Views:
867
Downloads:
104
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Record is a part of a journal
Title:
Plants
Shortened title:
Plants
Publisher:
MDPI
ISSN:
2223-7747
COBISS.SI-ID:
523345433
Licences
License:
CC BY 4.0, Creative Commons Attribution 4.0 International
Link:
http://creativecommons.org/licenses/by/4.0/
Description:
This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
Licensing start date:
01.04.2021
Secondary language
Language:
Slovenian
Keywords:
analiza omrežij
,
fitoplazme
,
počrnelost lesa
Projects
Funder:
ARRS - Slovenian Research Agency
Project number:
J1-7151
Name:
Molekulske osnove interakcij med vinsko trto in fitoplazemskimi povzročiteljicami trsnih rumenic
Funder:
ARRS - Slovenian Research Agency
Project number:
N2-0078
Name:
Semantično rudarjenje prostodostopnih povezanih podatkov
Funder:
ARRS - Slovenian Research Agency
Project number:
P2-0103
Name:
Tehnologije znanja
Funder:
ARRS - Slovenian Research Agency
Funding programme:
Young researcher
Funder:
FWF - Austrian Science Fund
Project number:
I 2763-B29
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