Research output: Contribution to journal › Article › peer-review
Prioritization of biological processes based on the reconstruction and analysis of associative gene networks describing the response of plants to adverse environmental factors. / Demenkov, P. S.; Oshchepkova, E. A.; Ivanisenko, T. V. et al.
In: Vavilovskii Zhurnal Genetiki i Selektsii, Vol. 25, No. 5, 13, 09.2021, p. 580-592.Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - Prioritization of biological processes based on the reconstruction and analysis of associative gene networks describing the response of plants to adverse environmental factors
AU - Demenkov, P. S.
AU - Oshchepkova, E. A.
AU - Ivanisenko, T. V.
AU - Ivanisenko, V. A.
N1 - Funding Information: Reconstruction and analysis of associative gene networks were carried out within the framework of the ICG SB RAS project ?Creation of new competitive potato varieties using marker-based and genomic selection methods?(AAAA-A20-120070990014-7) within the framework of the KPNI?Development of potato breeding and seed production?. The development of prioritization methods was carried out at the expense of the budget projects 0259-2021-0009 and 0259-2021-0012. Publisher Copyright: © Demenkov P.S., Oshchepkova Е.А., Ivanisenko T.V., Ivanisenko V.A., 2021 This work is licensed under a Creative Commons Attribution 4.0 License
PY - 2021/9
Y1 - 2021/9
N2 - Methods for prioritizing or ranking candidate genes according to their importance based on specific criteria via the analysis of gene networks are widely used in biomedicine to search for genes associated with diseases and to predict biomarkers, pharmacological targets and other clinically relevant molecules. These methods have also been used in other fields, particularly in crop production. This is largely due to the development of technologies to solve problems in marker-oriented and genomic selection, which requires knowledge of the molecular genetic mechanisms underlying the formation of agriculturally valuable traits. A new direction for the study of molecular genetic mechanisms is the prioritization of biological processes based on the analysis of associative gene networks. Associative gene networks are heterogeneous networks whose vertices can depict both molecular genetic objects (genes, proteins, metabolites, etc.) and the higher-level factors (biological processes, diseases, external environmental factors, etc.) related to regulatory, physicochemical or associative interactions. Using a previously developed method, biological processes involved in plant responses to increased cadmium content, saline stress and drought conditions were prioritized according to their degree of connection with the gene networks in the SOLANUM TUBEROSUM knowledge base. The prioritization results indicate that fundamental processes, such as gene expression, post-translational modifications, protein degradation, programmed cell death, photosynthesis, signal transmission and stress response play important roles in the common molecular genetic mechanisms for plant response to various adverse factors. On the other hand, a group of processes related to the development of seeds (“seeding development”) was revealed to be drought specific, while processes associated with ion transport (“ion transport”) were included in the list of responses specific to salt stress and processes associated with the metabolism of lipids were found to be involved specifically in the response to cadmium.
AB - Methods for prioritizing or ranking candidate genes according to their importance based on specific criteria via the analysis of gene networks are widely used in biomedicine to search for genes associated with diseases and to predict biomarkers, pharmacological targets and other clinically relevant molecules. These methods have also been used in other fields, particularly in crop production. This is largely due to the development of technologies to solve problems in marker-oriented and genomic selection, which requires knowledge of the molecular genetic mechanisms underlying the formation of agriculturally valuable traits. A new direction for the study of molecular genetic mechanisms is the prioritization of biological processes based on the analysis of associative gene networks. Associative gene networks are heterogeneous networks whose vertices can depict both molecular genetic objects (genes, proteins, metabolites, etc.) and the higher-level factors (biological processes, diseases, external environmental factors, etc.) related to regulatory, physicochemical or associative interactions. Using a previously developed method, biological processes involved in plant responses to increased cadmium content, saline stress and drought conditions were prioritized according to their degree of connection with the gene networks in the SOLANUM TUBEROSUM knowledge base. The prioritization results indicate that fundamental processes, such as gene expression, post-translational modifications, protein degradation, programmed cell death, photosynthesis, signal transmission and stress response play important roles in the common molecular genetic mechanisms for plant response to various adverse factors. On the other hand, a group of processes related to the development of seeds (“seeding development”) was revealed to be drought specific, while processes associated with ion transport (“ion transport”) were included in the list of responses specific to salt stress and processes associated with the metabolism of lipids were found to be involved specifically in the response to cadmium.
KW - Arabidopsis thaliana
KW - Associative gene networks
KW - Centrality of vertices
KW - Gene ontology
KW - Knowledge base solanum tuberosum
KW - Network-based prioritization methods
KW - Text mining methods
UR - http://www.scopus.com/inward/record.url?scp=85115769101&partnerID=8YFLogxK
UR - https://elibrary.ru/item.asp?id=46532288
U2 - 10.18699/VJ21.065
DO - 10.18699/VJ21.065
M3 - Article
C2 - 34723066
AN - SCOPUS:85115769101
VL - 25
SP - 580
EP - 592
JO - Вавиловский журнал генетики и селекции
JF - Вавиловский журнал генетики и селекции
SN - 2500-0462
IS - 5
M1 - 13
ER -
ID: 34338848