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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Main Authors: Reagan Mudziwapasi, Ryman Shoko, Babra Magogo, Jessica Pullen, Joice Ndlovu
Other Authors: Department of Research and Innovation, Midlands State University, Gweru, Zimbabwe.
Format: research article
Language:English
Published: Taylor and Francis Ltd 2023
Subjects:
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
collection DSpace
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.
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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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