Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data
Proteins rarely carry out their cellular functions in isolation. Instead, eukaryotic proteins engage in about six interactions with other proteins on average. The aggregated protein interactome of an organism forms a “hairy ball”-type protein-protein interaction (PPI) network. Yet, in a typical huma...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-09-01
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| Series: | Frontiers in Bioinformatics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2021.724297/full |
| _version_ | 1818733913625853952 |
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| author | Markus Hollander Trang Do Thorsten Will Volkhard Helms |
| author_facet | Markus Hollander Trang Do Thorsten Will Volkhard Helms |
| author_sort | Markus Hollander |
| collection | DOAJ |
| description | Proteins rarely carry out their cellular functions in isolation. Instead, eukaryotic proteins engage in about six interactions with other proteins on average. The aggregated protein interactome of an organism forms a “hairy ball”-type protein-protein interaction (PPI) network. Yet, in a typical human cell, only about half of all proteins are expressed at a particular time. Hence, it has become common practice to prune the full PPI network to the subset of expressed proteins. If RNAseq data is available, one can further resolve the specific protein isoforms present in a cell or tissue. Here, we review various approaches, software tools and webservices that enable users to construct context-specific or tissue-specific PPI networks and how these are rewired between two cellular conditions. We illustrate their different functionalities on the example of the interactions involving the human TNR6 protein. In an outlook, we describe how PPI networks may be integrated with epigenetic data or with data on the activity of splicing factors. |
| first_indexed | 2024-12-17T23:57:01Z |
| format | Article |
| id | doaj.art-b279d0c8b2ab4eebbe72f3ad0c30509f |
| institution | Directory Open Access Journal |
| issn | 2673-7647 |
| language | English |
| last_indexed | 2024-12-17T23:57:01Z |
| publishDate | 2021-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj.art-b279d0c8b2ab4eebbe72f3ad0c30509f2022-12-21T21:28:02ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472021-09-01110.3389/fbinf.2021.724297724297Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic DataMarkus HollanderTrang DoThorsten WillVolkhard HelmsProteins rarely carry out their cellular functions in isolation. Instead, eukaryotic proteins engage in about six interactions with other proteins on average. The aggregated protein interactome of an organism forms a “hairy ball”-type protein-protein interaction (PPI) network. Yet, in a typical human cell, only about half of all proteins are expressed at a particular time. Hence, it has become common practice to prune the full PPI network to the subset of expressed proteins. If RNAseq data is available, one can further resolve the specific protein isoforms present in a cell or tissue. Here, we review various approaches, software tools and webservices that enable users to construct context-specific or tissue-specific PPI networks and how these are rewired between two cellular conditions. We illustrate their different functionalities on the example of the interactions involving the human TNR6 protein. In an outlook, we describe how PPI networks may be integrated with epigenetic data or with data on the activity of splicing factors.https://www.frontiersin.org/articles/10.3389/fbinf.2021.724297/fulltranscriptomicsdomain-domain interaction (DDI)protein-protein interaction (PPI)isoformalternative splicing (AS) events |
| spellingShingle | Markus Hollander Trang Do Thorsten Will Volkhard Helms Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data Frontiers in Bioinformatics transcriptomics domain-domain interaction (DDI) protein-protein interaction (PPI) isoform alternative splicing (AS) events |
| title | Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data |
| title_full | Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data |
| title_fullStr | Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data |
| title_full_unstemmed | Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data |
| title_short | Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data |
| title_sort | detecting rewiring events in protein protein interaction networks based on transcriptomic data |
| topic | transcriptomics domain-domain interaction (DDI) protein-protein interaction (PPI) isoform alternative splicing (AS) events |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2021.724297/full |
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