Topological Structure Analysis of the Protein-protein Interaction Network in Budding Yeast

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2003 Apr 25

PMID 12711690

Citations 95

Authors

Dongbo Bu

Yi Zhao

Lun Cai

Hong Xue

Xiaopeng Zhu

Hongchao Lu

Jingfen Zhang

Shiwei Sun

Lunjiang Ling

Nan Zhang

Guojie Li

Runsheng Chen

Affiliations

Soon will be listed here.

Abstract

Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here, a spectral method derived from graph theory was introduced to uncover hidden topological structures (i.e. quasi-cliques and quasi-bipartites) of complicated protein-protein interaction networks. Our analyses suggest that these hidden topological structures consist of biologically relevant functional groups. This result motivates a new method to predict the function of uncharacterized proteins based on the classification of known proteins within topological structures. Using this spectral analysis method, 48 quasi-cliques and six quasi-bipartites were isolated from a network involving 11,855 interactions among 2617 proteins in budding yeast, and 76 uncharacterized proteins were assigned functions.

Citing Articles

A novel voting measure for identifying influential nodes in complex networks based on local structure.

Li H, Wang X, Chen Y, Cheng S, Lu D Sci Rep. 2025; 15(1):1693.

PMID: 39799212 PMC: 11724906. DOI: 10.1038/s41598-025-85332-4.

Synergistic Integration of Local and Global Information for Critical Edge Identification.

Zhao N, Luo T, Wang H, Yang S, Xiong N, Jing M Entropy (Basel). 2024; 26(11).

PMID: 39593878 PMC: 11592678. DOI: 10.3390/e26110933.

Integrating local and global information to identify influential nodes in complex networks.

Mukhtar M, Abal Abas Z, Baharuddin A, Norizan M, Fakhruddin W, Minato W Sci Rep. 2023; 13(1):11411.

PMID: 37452080 PMC: 10349046. DOI: 10.1038/s41598-023-37570-7.

Identification of Targeted Central Genes (IGF1 and HMOX1) by Indirect Cold Physical Plasma in Human Melanocytes.

Vafaee R, Arjmand B, Hamzeloo-Moghadam M, Razzaghi Z, Rezaei Tavirani M, Rezaei Tavirani S J Lasers Med Sci. 2023; 13:e70.

PMID: 37041797 PMC: 10082895. DOI: 10.34172/jlms.2022.70.

Data Incompleteness May form a Hard-to-Overcome Barrier to Decoding Life's Mechanism.

Kondratyeva L, Alekseenko I, Chernov I, Sverdlov E Biology (Basel). 2022; 11(8).

PMID: 36009835 PMC: 9404739. DOI: 10.3390/biology11081208.

References

Cho R, Campbell M, Winzeler E, Steinmetz L, Conway A, Wodicka L . A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell. 1998; 2(1):65-73. DOI: 10.1016/s1097-2765(00)80114-8. View

Watts D, Strogatz S . Collective dynamics of 'small-world' networks. Nature. 1998; 393(6684):440-2. DOI: 10.1038/30918. View

Overbeek R, Fonstein M, DSouza M, Pusch G, Maltsev N . The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A. 1999; 96(6):2896-901. PMC: 15866. DOI: 10.1073/pnas.96.6.2896. View

Pellegrini M, Marcotte E, Thompson M, Eisenberg D, Yeates T . Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A. 1999; 96(8):4285-8. PMC: 16324. DOI: 10.1073/pnas.96.8.4285. View

Tavazoie S, Hughes J, Campbell M, Cho R, Church G . Systematic determination of genetic network architecture. Nat Genet. 1999; 22(3):281-5. DOI: 10.1038/10343. View

Marcotte E, Pellegrini M, Ng H, Rice D, Yeates T, Eisenberg D . Detecting protein function and protein-protein interactions from genome sequences. Science. 1999; 285(5428):751-3. DOI: 10.1126/science.285.5428.751. View

Enright A, Iliopoulos I, Kyrpides N, Ouzounis C . Protein interaction maps for complete genomes based on gene fusion events. Nature. 1999; 402(6757):86-90. DOI: 10.1038/47056. View

Uetz P, Giot L, Cagney G, Mansfield T, Judson R, Knight J . A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000; 403(6770):623-7. DOI: 10.1038/35001009. View

Hughes T, Marton M, Jones A, Roberts C, STOUGHTON R, Armour C . Functional discovery via a compendium of expression profiles. Cell. 2000; 102(1):109-26. DOI: 10.1016/s0092-8674(00)00015-5. View

10.

Schwikowski B, Uetz P, Fields S . A network of protein-protein interactions in yeast. Nat Biotechnol. 2000; 18(12):1257-61. DOI: 10.1038/82360. View

11.

Rain J, Selig L, de Reuse H, Battaglia V, Reverdy C, Simon S . The protein-protein interaction map of Helicobacter pylori. Nature. 2001; 409(6817):211-5. DOI: 10.1038/35051615. View

12.

Hishigaki H, Nakai K, Ono T, Tanigami A, Takagi T . Assessment of prediction accuracy of protein function from protein--protein interaction data. Yeast. 2001; 18(6):523-31. DOI: 10.1002/yea.706. View

13.

Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y . A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A. 2001; 98(8):4569-74. PMC: 31875. DOI: 10.1073/pnas.061034498. View

14.

Harnpicharnchai P, Jakovljevic J, Horsey E, Miles T, Roman J, Rout M . Composition and functional characterization of yeast 66S ribosome assembly intermediates. Mol Cell. 2001; 8(3):505-15. DOI: 10.1016/s1097-2765(01)00344-6. View

15.

Bassler J, Grandi P, Gadal O, Lessmann T, Petfalski E, Tollervey D . Identification of a 60S preribosomal particle that is closely linked to nuclear export. Mol Cell. 2001; 8(3):517-29. DOI: 10.1016/s1097-2765(01)00342-2. View

16.

Ge H, Liu Z, Church G, Vidal M . Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet. 2001; 29(4):482-6. DOI: 10.1038/ng776. View

17.

Tong A, Evangelista M, Parsons A, Xu H, Bader G, Page N . Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 2001; 294(5550):2364-8. DOI: 10.1126/science.1065810. View

18.

Mewes H, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M . MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 2001; 30(1):31-4. PMC: 99165. DOI: 10.1093/nar/30.1.31. View

19.

Gavin A, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A . Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002; 415(6868):141-7. DOI: 10.1038/415141a. View

20.

Ho Y, Gruhler A, Heilbut A, Bader G, Moore L, Adams S . Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002; 415(6868):180-3. DOI: 10.1038/415180a. View