Protein-protein interaction network of E. coli K-12 has significant high-dimensional cavities : new insights from algebraic topological studies
© 2022 The Authors. FEBS Open Bio published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies..
As a model system, Escherichia coli has been used to study various life processes. A dramatic paradigm shift has occurred in recent years, with the study of single proteins moving toward the study of dynamically interacting proteins, especially protein-protein interaction (PPI) networks. However, despite the importance of PPI networks, little is known about the intrinsic nature of the network structure, especially high-dimensional topological properties. By introducing general hypergeometric distribution, we reconstruct a statistically reliable combined PPI network of E. coli (E. coli-PPI-Network) from several datasets. Unlike traditional graph analysis, algebraic topology was introduced to analyze the topological structures of the E. coli-PPI-Network, including high-dimensional cavities and cycles. Random networks with the same node and edge number (RandomNet) or scale-free networks with the same degree distribution (RandomNet-SameDD) were produced as controls. We discovered that the E. coli-PPI-Network had special algebraic typological structures, exhibiting more high-dimensional cavities and cycles, compared to RandomNets or, importantly, RandomNet-SameDD. Based on these results, we defined degree of involved q-dimensional cycles of proteins (q-DCprotein ) in the network, a novel concept that relies on the integral structure of the network and is different from traditional node degree or hubs. Finally, top proteins ranked by their 1-DCprotein were identified (such as gmhB, rpoA, rplB, rpsF and yfgB). In conclusion, by introducing mathematical and computer technologies, we discovered novel algebraic topological properties of the E. coli-PPI-Network, which has special high-dimensional cavities and cycles, and thereby revealed certain intrinsic rules of information flow underlining bacteria biology.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:12 |
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| Enthalten in: |
FEBS open bio - 12(2022), 7 vom: 21. Juli, Seite 1406-1418 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Xue, Xiao-Yan [VerfasserIn] |
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| Links: |
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| Themen: |
Betti number |
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| Anmerkungen: |
Date Completed 06.07.2022 Date Revised 15.09.2022 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1002/2211-5463.13437 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM34083949X |
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| 520 | |a © 2022 The Authors. FEBS Open Bio published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies. | ||
| 520 | |a As a model system, Escherichia coli has been used to study various life processes. A dramatic paradigm shift has occurred in recent years, with the study of single proteins moving toward the study of dynamically interacting proteins, especially protein-protein interaction (PPI) networks. However, despite the importance of PPI networks, little is known about the intrinsic nature of the network structure, especially high-dimensional topological properties. By introducing general hypergeometric distribution, we reconstruct a statistically reliable combined PPI network of E. coli (E. coli-PPI-Network) from several datasets. Unlike traditional graph analysis, algebraic topology was introduced to analyze the topological structures of the E. coli-PPI-Network, including high-dimensional cavities and cycles. Random networks with the same node and edge number (RandomNet) or scale-free networks with the same degree distribution (RandomNet-SameDD) were produced as controls. We discovered that the E. coli-PPI-Network had special algebraic typological structures, exhibiting more high-dimensional cavities and cycles, compared to RandomNets or, importantly, RandomNet-SameDD. Based on these results, we defined degree of involved q-dimensional cycles of proteins (q-DCprotein ) in the network, a novel concept that relies on the integral structure of the network and is different from traditional node degree or hubs. Finally, top proteins ranked by their 1-DCprotein were identified (such as gmhB, rpoA, rplB, rpsF and yfgB). In conclusion, by introducing mathematical and computer technologies, we discovered novel algebraic topological properties of the E. coli-PPI-Network, which has special high-dimensional cavities and cycles, and thereby revealed certain intrinsic rules of information flow underlining bacteria biology | ||
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| 700 | 1 | |a Nie, Dan |e verfasserin |4 aut | |
| 700 | 1 | |a Zhao, Hui |e verfasserin |4 aut | |
| 700 | 1 | |a Mao, Xing-Gang |e verfasserin |4 aut | |
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