Drought Stress-Related Gene Identification in Rice by Random Walk with Restart on Multiplex Biological Networks
Drought stress-related gene identification is vital in revealing the drought resistance mechanisms underlying rice and for cultivating rice-resistant varieties. Traditional methods, such as Genome-Wide Association Studies (GWAS), usually identify hundreds of candidate stress genes, and further valid...
| Main Authors: | , , , , , , |
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| Format: | Article |
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MDPI AG
2022-12-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/13/1/53 |
| _version_ | 1797447319195484160 |
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| author | Liu Zhu Hongyan Zhang Dan Cao Yalan Xu Lanzhi Li Zilan Ning Lei Zhu |
| author_facet | Liu Zhu Hongyan Zhang Dan Cao Yalan Xu Lanzhi Li Zilan Ning Lei Zhu |
| author_sort | Liu Zhu |
| collection | DOAJ |
| description | Drought stress-related gene identification is vital in revealing the drought resistance mechanisms underlying rice and for cultivating rice-resistant varieties. Traditional methods, such as Genome-Wide Association Studies (GWAS), usually identify hundreds of candidate stress genes, and further validation by biological experiements is then time-consuming and laborious. However, computational and prioritization methods can effectively reduce the number of candidate stress genes. This study introduces a random walk with restart algorithm (RWR), a state-of-the-art guilt-by-association method, to operate on rice multiplex biological networks. It explores the physical and functional interactions between biological molecules at different levels and prioritizes a set of potential genes. Firstly, we integrated a Protein–Protein Interaction (PPI) network, constructed by multiple protein interaction data, with a gene coexpression network into a multiplex network. Then, we implemented the RWR on multiplex networks (RWR-M) with known drought stress genes as seed nodes to identify potential drought stress-related genes. Finally, we conducted association analysis between the potential genes and the known drought stress genes. Thirteen genes were identified as rice drought stress-related genes, five of which have been reported in the recent literature to be involved in drought stress resistance mechanisms. |
| first_indexed | 2024-03-09T13:54:14Z |
| format | Article |
| id | doaj.art-9c0153eda27640459bad9a0817e59885 |
| institution | Directory Open Access Journal |
| issn | 2077-0472 |
| language | English |
| last_indexed | 2024-03-09T13:54:14Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agriculture |
| spelling | doaj.art-9c0153eda27640459bad9a0817e598852023-11-30T20:45:00ZengMDPI AGAgriculture2077-04722022-12-011315310.3390/agriculture13010053Drought Stress-Related Gene Identification in Rice by Random Walk with Restart on Multiplex Biological NetworksLiu Zhu0Hongyan Zhang1Dan Cao2Yalan Xu3Lanzhi Li4Zilan Ning5Lei Zhu6College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, ChinaCollege of Information and Intelligence, Hunan Agricultural University, Changsha 410128, ChinaCollege of Science, Central South University of Forestry and Technology, Changsha 410004, ChinaCollege of Information and Intelligence, Hunan Agricultural University, Changsha 410128, ChinaHunan Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Hunan Agricultural University, Changsha 410128, ChinaCollege of Information and Intelligence, Hunan Agricultural University, Changsha 410128, ChinaCollege of Information and Intelligence, Hunan Agricultural University, Changsha 410128, ChinaDrought stress-related gene identification is vital in revealing the drought resistance mechanisms underlying rice and for cultivating rice-resistant varieties. Traditional methods, such as Genome-Wide Association Studies (GWAS), usually identify hundreds of candidate stress genes, and further validation by biological experiements is then time-consuming and laborious. However, computational and prioritization methods can effectively reduce the number of candidate stress genes. This study introduces a random walk with restart algorithm (RWR), a state-of-the-art guilt-by-association method, to operate on rice multiplex biological networks. It explores the physical and functional interactions between biological molecules at different levels and prioritizes a set of potential genes. Firstly, we integrated a Protein–Protein Interaction (PPI) network, constructed by multiple protein interaction data, with a gene coexpression network into a multiplex network. Then, we implemented the RWR on multiplex networks (RWR-M) with known drought stress genes as seed nodes to identify potential drought stress-related genes. Finally, we conducted association analysis between the potential genes and the known drought stress genes. Thirteen genes were identified as rice drought stress-related genes, five of which have been reported in the recent literature to be involved in drought stress resistance mechanisms.https://www.mdpi.com/2077-0472/13/1/53riceprotein–protein interactioncoexpression networkdrought stress generandom walk with restart |
| spellingShingle | Liu Zhu Hongyan Zhang Dan Cao Yalan Xu Lanzhi Li Zilan Ning Lei Zhu Drought Stress-Related Gene Identification in Rice by Random Walk with Restart on Multiplex Biological Networks Agriculture rice protein–protein interaction coexpression network drought stress gene random walk with restart |
| title | Drought Stress-Related Gene Identification in Rice by Random Walk with Restart on Multiplex Biological Networks |
| title_full | Drought Stress-Related Gene Identification in Rice by Random Walk with Restart on Multiplex Biological Networks |
| title_fullStr | Drought Stress-Related Gene Identification in Rice by Random Walk with Restart on Multiplex Biological Networks |
| title_full_unstemmed | Drought Stress-Related Gene Identification in Rice by Random Walk with Restart on Multiplex Biological Networks |
| title_short | Drought Stress-Related Gene Identification in Rice by Random Walk with Restart on Multiplex Biological Networks |
| title_sort | drought stress related gene identification in rice by random walk with restart on multiplex biological networks |
| topic | rice protein–protein interaction coexpression network drought stress gene random walk with restart |
| url | https://www.mdpi.com/2077-0472/13/1/53 |
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