ANALYSIS OF THE INTERACTIONS OF NEURONAL APOPTOSIS GENES IN THE ASSOCIATIVE GENE NETWORK OF PARKINSON’S DISEASE
Parkinson’s disease (PD) affects an estimated 7–10 million people worldwide and 210000 people in Russia. PD is accompanied by degeneration of dopaminergic neurons and because of that neuronal apoptosis is an important factor in this disease. Analysis of gene networks is one of the key approaches in...
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| Format: | Article |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2018-03-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/1376 |
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| author | M. A. Yankina O. V. Saik P. S. Demenkov E. K. Khusnutdinova E. I. Rogaev I. N. Lavrik V. А. Ivanisenko |
| author_facet | M. A. Yankina O. V. Saik P. S. Demenkov E. K. Khusnutdinova E. I. Rogaev I. N. Lavrik V. А. Ivanisenko |
| author_sort | M. A. Yankina |
| collection | DOAJ |
| description | Parkinson’s disease (PD) affects an estimated 7–10 million people worldwide and 210000 people in Russia. PD is accompanied by degeneration of dopaminergic neurons and because of that neuronal apoptosis is an important factor in this disease. Analysis of gene networks is one of the key approaches in systems biology. We previously developed the ANDSystem tool, designed to automatically extract knowledge from scientific publications and reconstruct on this basis associative gene networks describing the molecular genetic mechanisms of biological processes. The aim of this work was prioritization of neuronal apoptosis genes by their involvement in PD pathogenesis, taking into account the structure of the PD associative gene network using ANDSystem. Analysis of the centrality of neuronal apoptosis genes, associated with PD, revealed that mean values of degree, closeness and betweenness centralities statistically significantly exceed such values of all nodes of the PD network. The APOE, CASP3 and GAPDH genes involved in neuronal apoptosis were among the most central genes. Prioritization of neuronal apoptosis genes for which there was no data in ANDSystem on their associations with PD was performed using standard methods (Endeavor and ToppGene) and the criteria of centrality and specificity of genes interactions with the PD gene network. Analysis revealed that genes involved in such processes as positive and negative regulation of neu ronal apoptosis, MAPK and ephrin receptor signaling pathways, are mainly represented among candidate genes with the highest priority (top 50, 70, 100 genes were considered). In particular, TP53, JUN, BCL2, PIK3CA and APP were among candidate genes with the highest priority. |
| format | Article |
| id | doaj-art-b7401a15e2b7481d8b832e498ca7d1d3 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2018-03-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-b7401a15e2b7481d8b832e498ca7d1d32025-02-01T09:58:05ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592018-03-0122115316010.18699/VJ18.343735ANALYSIS OF THE INTERACTIONS OF NEURONAL APOPTOSIS GENES IN THE ASSOCIATIVE GENE NETWORK OF PARKINSON’S DISEASEM. A. Yankina0O. V. Saik1P. S. Demenkov2E. K. Khusnutdinova3E. I. Rogaev4I. N. Lavrik5V. А. Ivanisenko6Institute of Biochemistry and Genetics, Ufa Research Centre RASInstitute of Cytology and Genetics SB RASInstitute of Cytology and Genetics SB RASInstitute of Biochemistry and Genetics, Ufa Research Centre RAS; Bashkir State UniversityInstitute of Cytology and Genetics SB RAS; University of Massachusetts Medical School; Institute of General Genetics RAS; Lomonosov Moscow State UniversityInstitute of Cytology and Genetics SB RAS; Otto von Guericke UniversityInstitute of Cytology and Genetics SB RASParkinson’s disease (PD) affects an estimated 7–10 million people worldwide and 210000 people in Russia. PD is accompanied by degeneration of dopaminergic neurons and because of that neuronal apoptosis is an important factor in this disease. Analysis of gene networks is one of the key approaches in systems biology. We previously developed the ANDSystem tool, designed to automatically extract knowledge from scientific publications and reconstruct on this basis associative gene networks describing the molecular genetic mechanisms of biological processes. The aim of this work was prioritization of neuronal apoptosis genes by their involvement in PD pathogenesis, taking into account the structure of the PD associative gene network using ANDSystem. Analysis of the centrality of neuronal apoptosis genes, associated with PD, revealed that mean values of degree, closeness and betweenness centralities statistically significantly exceed such values of all nodes of the PD network. The APOE, CASP3 and GAPDH genes involved in neuronal apoptosis were among the most central genes. Prioritization of neuronal apoptosis genes for which there was no data in ANDSystem on their associations with PD was performed using standard methods (Endeavor and ToppGene) and the criteria of centrality and specificity of genes interactions with the PD gene network. Analysis revealed that genes involved in such processes as positive and negative regulation of neu ronal apoptosis, MAPK and ephrin receptor signaling pathways, are mainly represented among candidate genes with the highest priority (top 50, 70, 100 genes were considered). In particular, TP53, JUN, BCL2, PIK3CA and APP were among candidate genes with the highest priority.https://vavilov.elpub.ru/jour/article/view/1376neuronal apoptosisparkinson’s diseaseandsystemassociative gene networks |
| spellingShingle | M. A. Yankina O. V. Saik P. S. Demenkov E. K. Khusnutdinova E. I. Rogaev I. N. Lavrik V. А. Ivanisenko ANALYSIS OF THE INTERACTIONS OF NEURONAL APOPTOSIS GENES IN THE ASSOCIATIVE GENE NETWORK OF PARKINSON’S DISEASE Вавиловский журнал генетики и селекции neuronal apoptosis parkinson’s disease andsystem associative gene networks |
| title | ANALYSIS OF THE INTERACTIONS OF NEURONAL APOPTOSIS GENES IN THE ASSOCIATIVE GENE NETWORK OF PARKINSON’S DISEASE |
| title_full | ANALYSIS OF THE INTERACTIONS OF NEURONAL APOPTOSIS GENES IN THE ASSOCIATIVE GENE NETWORK OF PARKINSON’S DISEASE |
| title_fullStr | ANALYSIS OF THE INTERACTIONS OF NEURONAL APOPTOSIS GENES IN THE ASSOCIATIVE GENE NETWORK OF PARKINSON’S DISEASE |
| title_full_unstemmed | ANALYSIS OF THE INTERACTIONS OF NEURONAL APOPTOSIS GENES IN THE ASSOCIATIVE GENE NETWORK OF PARKINSON’S DISEASE |
| title_short | ANALYSIS OF THE INTERACTIONS OF NEURONAL APOPTOSIS GENES IN THE ASSOCIATIVE GENE NETWORK OF PARKINSON’S DISEASE |
| title_sort | analysis of the interactions of neuronal apoptosis genes in the associative gene network of parkinson s disease |
| topic | neuronal apoptosis parkinson’s disease andsystem associative gene networks |
| url | https://vavilov.elpub.ru/jour/article/view/1376 |
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