Gene Coexpression Network Comparison via Persistent Homology
Persistent homology, a topological data analysis (TDA) method, is applied to microarray data sets. Although there are a few papers referring to TDA methods in microarray analysis, the usage of persistent homology in the comparison of several weighted gene coexpression networks (WGCN) was not employe...
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| Format: | Article |
| Language: | English |
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Wiley
2018-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2018/7329576 |
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| _version_ | 1832563057392353280 |
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| author | Ali Nabi Duman Harun Pirim |
| author_facet | Ali Nabi Duman Harun Pirim |
| author_sort | Ali Nabi Duman |
| collection | DOAJ |
| description | Persistent homology, a topological data analysis (TDA) method, is applied to microarray data sets. Although there are a few papers referring to TDA methods in microarray analysis, the usage of persistent homology in the comparison of several weighted gene coexpression networks (WGCN) was not employed before to the very best of our knowledge. We calculate the persistent homology of weighted networks constructed from 38 Arabidopsis microarray data sets to test the relevance and the success of this approach in distinguishing the stress factors. We quantify multiscale topological features of each network using persistent homology and apply a hierarchical clustering algorithm to the distance matrix whose entries are pairwise bottleneck distance between the networks. The immunoresponses to different stress factors are distinguishable by our method. The networks of similar immunoresponses are found to be close with respect to bottleneck distance indicating the similar topological features of WGCNs. This computationally efficient technique analyzing networks provides a quick test for advanced studies. |
| format | Article |
| id | doaj-art-f992133b5e7244b28af837c2c407f1d2 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2018-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-f992133b5e7244b28af837c2c407f1d22025-02-03T01:21:14ZengWileyInternational Journal of Genomics2314-436X2314-43782018-01-01201810.1155/2018/73295767329576Gene Coexpression Network Comparison via Persistent HomologyAli Nabi Duman0Harun Pirim1Department of Mathematics and Statistics, King Fahd University of Petroleum and Minerals, Dhahran, Saudi ArabiaDepartment of Systems Engineering, King Fahd University of Petroleum and Minerals, Dhahran, Saudi ArabiaPersistent homology, a topological data analysis (TDA) method, is applied to microarray data sets. Although there are a few papers referring to TDA methods in microarray analysis, the usage of persistent homology in the comparison of several weighted gene coexpression networks (WGCN) was not employed before to the very best of our knowledge. We calculate the persistent homology of weighted networks constructed from 38 Arabidopsis microarray data sets to test the relevance and the success of this approach in distinguishing the stress factors. We quantify multiscale topological features of each network using persistent homology and apply a hierarchical clustering algorithm to the distance matrix whose entries are pairwise bottleneck distance between the networks. The immunoresponses to different stress factors are distinguishable by our method. The networks of similar immunoresponses are found to be close with respect to bottleneck distance indicating the similar topological features of WGCNs. This computationally efficient technique analyzing networks provides a quick test for advanced studies.http://dx.doi.org/10.1155/2018/7329576 |
| spellingShingle | Ali Nabi Duman Harun Pirim Gene Coexpression Network Comparison via Persistent Homology International Journal of Genomics |
| title | Gene Coexpression Network Comparison via Persistent Homology |
| title_full | Gene Coexpression Network Comparison via Persistent Homology |
| title_fullStr | Gene Coexpression Network Comparison via Persistent Homology |
| title_full_unstemmed | Gene Coexpression Network Comparison via Persistent Homology |
| title_short | Gene Coexpression Network Comparison via Persistent Homology |
| title_sort | gene coexpression network comparison via persistent homology |
| url | http://dx.doi.org/10.1155/2018/7329576 |
| work_keys_str_mv | AT alinabiduman genecoexpressionnetworkcomparisonviapersistenthomology AT harunpirim genecoexpressionnetworkcomparisonviapersistenthomology |