ANDVisio: A new tool for graphic visualization and analysis of literature mined associative gene networks in the ANDSystem

2012 ◽  
Vol 11 (3,4) ◽  
pp. 149-161 ◽  
Author(s):  
P.S. Demenkov ◽  
T.V. Ivanisenko ◽  
N.A. Kolchanov ◽  
V.A. Ivanisenko
Keyword(s):  
Gene Networks ◽  
Graphic Visualization ◽  
Associative Gene Networks

scholarly journals Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature

2018 ◽  
Vol 15 (4) ◽  
Author(s):  
Olga V. Saik ◽  
Pavel S. Demenkov ◽  
Timofey V. Ivanisenko ◽  
Elena Yu. Bragina ◽  
Maxim B. Freidin ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Molecular Genetic ◽  
Genetic Networks ◽  
Positive Sign ◽  
Phenotypic Traits ◽  
Protein Protein Interactions ◽  
Scientific Publications ◽  
Associative Gene Networks

AbstractComorbid states of diseases significantly complicate diagnosis and treatment. Molecular mechanisms of comorbid states of asthma and hypertension are still poorly understood. Prioritization is a way for identifying genes involved in complex phenotypic traits. Existing methods of prioritization consider genetic, expression and evolutionary data, molecular-genetic networks and other. In the case of molecular-genetic networks, as a rule, protein-protein interactions and KEGG networks are used. ANDSystem allows reconstructing associative gene networks, which include more than 20 types of interactions, including protein-protein interactions, expression regulation, transport, catalysis, etc. In this work, a set of genes has been prioritized to find genes potentially involved in asthma and hypertension comorbidity. The prioritization was carried out using well-known methods (ToppGene and Endeavor) and a cross-talk centrality criterion, calculated by analysis of associative gene networks from ANDSystem. The identified genes, including IL1A, CD40LG, STAT3, IL15, FAS, APP, TLR2, C3, IL13 and CXCL10, may be involved in the molecular mechanisms of comorbid asthma/hypertension. An analysis of the dynamics of the frequency of mentioning the most priority genes in scientific publications revealed that the top 100 priority genes are significantly enriched with genes with increased positive dynamics, which may be a positive sign for further studies of these genes.

scholarly journals Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks

2018 ◽  
Vol 11 (S1) ◽  
Author(s):  
Olga V. Saik ◽  
Pavel S. Demenkov ◽  
Timofey V. Ivanisenko ◽  
Elena Yu Bragina ◽  
Maxim B. Freidin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Gene Networks ◽  
Associative Gene Networks

scholarly journals Prioritization of genes involved in endothelial cell apoptosis by their implication in lymphedema using an analysis of associative gene networks with ANDSystem

2019 ◽  
Vol 12 (S2) ◽  
Author(s):  
Olga V. Saik ◽  
Vadim V. Nimaev ◽  
Dilovarkhuja B. Usmonov ◽  
Pavel S. Demenkov ◽  
Timofey V. Ivanisenko ◽  
...  
Keyword(s):  
Endothelial Cell ◽  
Cell Apoptosis ◽  
Gene Networks ◽  
Endothelial Cell Apoptosis ◽  
Associative Gene Networks

scholarly journals Prioritization of biological processes based on the reconstruction and analysis of associative gene networks describing the response of plants to adverse environmental factors

2021 ◽  
Vol 25 (5) ◽  
pp. 580-592
Author(s):  
P. S. Demenkov ◽  
E. A. Oshchepkova ◽  
T. V. Ivanisenko ◽  
V. A. Ivanisenko
Keyword(s):  
Environmental Factors ◽  
Ion Transport ◽  
Gene Networks ◽  
Crop Production ◽  
Molecular Genetic ◽  
Saline Stress ◽  
Cadmium Content ◽  
Biological Processes ◽  
Genetic Mechanisms ◽  
Associative Gene Networks

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, me tabolites, 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.

The economic strength and tax capacity of the Krasnoyarsk Krai: Challenges and the prospects for development

2020 ◽  
Vol 18 (4) ◽  
pp. 642-651
Author(s):  
V.V. Zozulya ◽  
I.S. Goryunova ◽  
I.V. Zozulya
Keyword(s):  
Sustainable Development ◽  
Import Substitution ◽  
Krasnoyarsk Krai ◽  
Resource Potential ◽  
The Sustainable Development ◽  
Comparative Analyses ◽  
Graphic Visualization ◽  
Further Development ◽  
Tax Capacity

Subject. The article discusses the prospects for the development of the Krasnoyarsk Krai and the implementation of the import substitution programme. Objectives. The article aims to analyze the tax potential of the Krasnoyarsk Krai, highlight the main problems, and identify possible directions for further development of the Krai. Methods. For the study, we used systems and institutional approaches, the methods of statistical and comparative analyses, and data tabular and graphic visualization. Results. The article identifies the main obstacles to the sustainable development of the Krasnoyarsk Krai. Conclusions. The Krasnoyarsk Krai has a strong economic and resource potential for further development, which is not being implemented properly.

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