Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow
Protein–protein interaction (PPI) is involved in every biological process that occurs within an organism. The understanding of PPI is essential for deciphering the cellular behaviours in a particular organism. The experimental data from PPI methods have been used in constructing the PPI network. PPI...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-04-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/12/5/650 |
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| author | Rabiatul-Adawiah Zainal-Abidin Nor Afiqah-Aleng Muhammad-Redha Abdullah-Zawawi Sarahani Harun Zeti-Azura Mohamed-Hussein |
| author_facet | Rabiatul-Adawiah Zainal-Abidin Nor Afiqah-Aleng Muhammad-Redha Abdullah-Zawawi Sarahani Harun Zeti-Azura Mohamed-Hussein |
| author_sort | Rabiatul-Adawiah Zainal-Abidin |
| collection | DOAJ |
| description | Protein–protein interaction (PPI) is involved in every biological process that occurs within an organism. The understanding of PPI is essential for deciphering the cellular behaviours in a particular organism. The experimental data from PPI methods have been used in constructing the PPI network. PPI network has been widely applied in biomedical research to understand the pathobiology of human diseases. It has also been used to understand the plant physiology that relates to crop improvement. However, the application of the PPI network in aquaculture is limited as compared to humans and plants. This review aims to demonstrate the workflow and step-by-step instructions for constructing a PPI network using bioinformatics tools and PPI databases that can help to predict potential interaction between proteins. We used zebrafish proteins, the oestrogen receptors (ERs) to build and analyse the PPI network. Thus, serving as a guide for future steps in exploring potential mechanisms on the organismal physiology of interest that ultimately benefit aquaculture research. |
| first_indexed | 2024-03-10T03:33:35Z |
| format | Article |
| id | doaj.art-361835373ac148cf9e011f05ea5a8257 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T03:33:35Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-361835373ac148cf9e011f05ea5a82572023-11-23T11:49:23ZengMDPI AGLife2075-17292022-04-0112565010.3390/life12050650Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics WorkflowRabiatul-Adawiah Zainal-Abidin0Nor Afiqah-Aleng1Muhammad-Redha Abdullah-Zawawi2Sarahani Harun3Zeti-Azura Mohamed-Hussein4Malaysian Agricultural Research & Development Institute (MARDI), Serdang 43400, MalaysiaInstitute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus 21030, MalaysiaUKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, MalaysiaCentre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, MalaysiaCentre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, MalaysiaProtein–protein interaction (PPI) is involved in every biological process that occurs within an organism. The understanding of PPI is essential for deciphering the cellular behaviours in a particular organism. The experimental data from PPI methods have been used in constructing the PPI network. PPI network has been widely applied in biomedical research to understand the pathobiology of human diseases. It has also been used to understand the plant physiology that relates to crop improvement. However, the application of the PPI network in aquaculture is limited as compared to humans and plants. This review aims to demonstrate the workflow and step-by-step instructions for constructing a PPI network using bioinformatics tools and PPI databases that can help to predict potential interaction between proteins. We used zebrafish proteins, the oestrogen receptors (ERs) to build and analyse the PPI network. Thus, serving as a guide for future steps in exploring potential mechanisms on the organismal physiology of interest that ultimately benefit aquaculture research.https://www.mdpi.com/2075-1729/12/5/650bioinformaticsoestrogen receptornetwork analysisprotein–protein interactionnetworkzebrafish |
| spellingShingle | Rabiatul-Adawiah Zainal-Abidin Nor Afiqah-Aleng Muhammad-Redha Abdullah-Zawawi Sarahani Harun Zeti-Azura Mohamed-Hussein Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow Life bioinformatics oestrogen receptor network analysis protein–protein interaction network zebrafish |
| title | Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow |
| title_full | Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow |
| title_fullStr | Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow |
| title_full_unstemmed | Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow |
| title_short | Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow |
| title_sort | protein protein interaction ppi network of zebrafish oestrogen receptors a bioinformatics workflow |
| topic | bioinformatics oestrogen receptor network analysis protein–protein interaction network zebrafish |
| url | https://www.mdpi.com/2075-1729/12/5/650 |
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