Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress
In order to understand the mechanism of desiccation tolerance in Xerophyta schlechteri, we carried out an in silico study to identify hub proteins and functional modules in the nuclear proteome of the leaves. Protein-protein interaction networks were constructed and analyzed from proteome data obtai...
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Taylor and Francis Ltd
2023
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Online Access: | https://cris.library.msu.ac.zw//handle/11408/5577 https://doi.org/10.1080/19420889.2023.2193000 |
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author | Reagan Mudziwapasi Ryman Shoko Babra Magogo Jessica Pullen Joice Ndlovu |
author2 | Department of Research and Innovation, Midlands State University, Gweru, Zimbabwe. |
author_facet | Department of Research and Innovation, Midlands State University, Gweru, Zimbabwe. Reagan Mudziwapasi Ryman Shoko Babra Magogo Jessica Pullen Joice Ndlovu |
author_sort | Reagan Mudziwapasi |
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description | In order to understand the mechanism of desiccation tolerance in Xerophyta schlechteri, we carried out an in silico study to identify hub proteins and functional modules in the nuclear proteome of the leaves. Protein-protein interaction networks were constructed and analyzed from proteome data obtained from Abdalla and Rafudeen. We constructed networks in Cytoscape using the GeneMania software and analyzed them using a Network Analyzer. Functional enrichment analysis of key proteins in the respective networks was done using GeneMania network enrichment analysis, and GO (Gene Ontology) terms were summarized using REViGO. Also, community analysis of differentially expressed proteins was conducted using the Cytoscape Apps, GeneMania and ClusterMaker. Functional modules associated with the communities were identified using an online tool, ShinyGO. We identified HSP 70-2 as the super-hub protein among the up-regulated proteins. On the other hand, 40S ribosomal protein S2-3 (a protein added by GeneMANIA) was identified as a super-hub protein associated with the down-regulated proteins. For up-regulated proteins, the enriched biological process terms were those associated with chromatin organization and negative regulation of transcription. In the down-regulated protein-set, terms associated with protein synthesis were significantly enriched. Community analysis identified three functional modules that can be categorized as chromatin organization, anti-oxidant activity and metabolic processes. |
format | research article |
id | ir-11408-5577 |
institution | My University |
language | English |
publishDate | 2023 |
publisher | Taylor and Francis Ltd |
record_format | dspace |
spelling | ir-11408-55772023-05-03T07:17:48Z Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress Reagan Mudziwapasi Ryman Shoko Babra Magogo Jessica Pullen Joice Ndlovu Department of Research and Innovation, Midlands State University, Gweru, Zimbabwe. Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe. Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe. Department of Animal Science and Rangeland Management, Lupane State University, Lupane, Zimbabwe. Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe. Bioinformatics Xerophyta schlechteri hub proteins protein–protein interaction resurrection plants In order to understand the mechanism of desiccation tolerance in Xerophyta schlechteri, we carried out an in silico study to identify hub proteins and functional modules in the nuclear proteome of the leaves. Protein-protein interaction networks were constructed and analyzed from proteome data obtained from Abdalla and Rafudeen. We constructed networks in Cytoscape using the GeneMania software and analyzed them using a Network Analyzer. Functional enrichment analysis of key proteins in the respective networks was done using GeneMania network enrichment analysis, and GO (Gene Ontology) terms were summarized using REViGO. Also, community analysis of differentially expressed proteins was conducted using the Cytoscape Apps, GeneMania and ClusterMaker. Functional modules associated with the communities were identified using an online tool, ShinyGO. We identified HSP 70-2 as the super-hub protein among the up-regulated proteins. On the other hand, 40S ribosomal protein S2-3 (a protein added by GeneMANIA) was identified as a super-hub protein associated with the down-regulated proteins. For up-regulated proteins, the enriched biological process terms were those associated with chromatin organization and negative regulation of transcription. In the down-regulated protein-set, terms associated with protein synthesis were significantly enriched. Community analysis identified three functional modules that can be categorized as chromatin organization, anti-oxidant activity and metabolic processes. 16 1 1 17 2023-05-03T07:17:48Z 2023-05-03T07:17:48Z 2023-03-22 research article https://cris.library.msu.ac.zw//handle/11408/5577 https://doi.org/10.1080/19420889.2023.2193000 en Communicative & Integrative Biology 1942-0889 open Taylor and Francis Ltd |
spellingShingle | Bioinformatics Xerophyta schlechteri hub proteins protein–protein interaction resurrection plants Reagan Mudziwapasi Ryman Shoko Babra Magogo Jessica Pullen Joice Ndlovu Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress |
title | Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress |
title_full | Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress |
title_fullStr | Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress |
title_full_unstemmed | Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress |
title_short | Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress |
title_sort | construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant xerophyta schlechteri leaves subjected to dehydration stress |
topic | Bioinformatics Xerophyta schlechteri hub proteins protein–protein interaction resurrection plants |
url | https://cris.library.msu.ac.zw//handle/11408/5577 https://doi.org/10.1080/19420889.2023.2193000 |
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