Efficient Prediction of Human Protein-protein Interactions at a Global Scale

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2014 Dec 11

PMID 25492630

Citations 16

Authors

Andrew Schoenrock

Bahram Samanfar

Sylvain Pitre

Mohsen Hooshyar

Ke Jin

Charles A Phillips

Hui Wang

Sadhna Phanse

Katayoun Omidi

Yuan Gui

Md Alamgir

Alex Wong

Fredrik Barrenas

Mohan Babu

Mikael Benson

Michael A Langston

James R Green

Frank Dehne

Ashkan Golshani

Affiliations

Soon will be listed here.

Abstract

Background: Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods.

Results: On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments.

Conclusions: The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.

Citing Articles

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References

Park Y . Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences. BMC Bioinformatics. 2009; 10:419. PMC: 2803199. DOI: 10.1186/1471-2105-10-419. View

Qi Y, Bar-Joseph Z, Klein-Seetharaman J . Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins. 2006; 63(3):490-500. PMC: 3250929. DOI: 10.1002/prot.20865. View

Dezso Z, Nikolsky Y, Nikolskaya T, Miller J, Cherba D, Webb C . Identifying disease-specific genes based on their topological significance in protein networks. BMC Syst Biol. 2009; 3:36. PMC: 2678983. DOI: 10.1186/1752-0509-3-36. View

Easton D, Ford D, Bishop D . Breast and ovarian cancer incidence in BRCA1-mutation carriers. Breast Cancer Linkage Consortium. Am J Hum Genet. 1995; 56(1):265-71. PMC: 1801337. View

Yu S, Vincent A, Opriessnig T, Carpenter S, Kitikoon P, Halbur P . Quantification of PCV2 capsid transcript in peripheral blood mononuclear cells (PBMCs) in vitro. Vet Microbiol. 2007; 123(1-3):34-42. DOI: 10.1016/j.vetmic.2007.02.021. View

Garcia-Gomez J, Lebaron S, Froment C, Monsarrat B, Henry Y, de la Cruz J . Dynamics of the putative RNA helicase Spb4 during ribosome assembly in Saccharomyces cerevisiae. Mol Cell Biol. 2011; 31(20):4156-64. PMC: 3187284. DOI: 10.1128/MCB.05436-11. View

Houvras Y, Benezra M, Zhang H, Manfredi J, Weber B, Licht J . BRCA1 physically and functionally interacts with ATF1. J Biol Chem. 2000; 275(46):36230-7. DOI: 10.1074/jbc.M002539200. View

Yosef N, Regev A . Impulse control: temporal dynamics in gene transcription. Cell. 2011; 144(6):886-96. PMC: 3148525. DOI: 10.1016/j.cell.2011.02.015. View

Ryser S, Dizin E, Jefford C, Delaval B, Gagos S, Christodoulidou A . Distinct roles of BARD1 isoforms in mitosis: full-length BARD1 mediates Aurora B degradation, cancer-associated BARD1beta scaffolds Aurora B and BRCA2. Cancer Res. 2009; 69(3):1125-34. DOI: 10.1158/0008-5472.CAN-08-2134. View

10.

Goh K, Cusick M, Valle D, Childs B, Vidal M, Barabasi A . The human disease network. Proc Natl Acad Sci U S A. 2007; 104(21):8685-90. PMC: 1885563. DOI: 10.1073/pnas.0701361104. View

11.

Wu J, Lu L, Yu X . The role of BRCA1 in DNA damage response. Protein Cell. 2011; 1(2):117-23. PMC: 3078634. DOI: 10.1007/s13238-010-0010-5. View

12.

Yu H, Kim P, Sprecher E, Trifonov V, Gerstein M . The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol. 2007; 3(4):e59. PMC: 1853125. DOI: 10.1371/journal.pcbi.0030059. View

13.

Benson M, Strannegard I, Strannegard O, Wennergren G . Topical steroid treatment of allergic rhinitis decreases nasal fluid TH2 cytokines, eosinophils, eosinophil cationic protein, and IgE but has no significant effect on IFN-gamma, IL-1beta, TNF-alpha, or neutrophils. J Allergy Clin Immunol. 2000; 106(2):307-12. DOI: 10.1067/mai.2000.108111. View

14.

Hans F, Skoufias D, Dimitrov S, Margolis R . Molecular distinctions between Aurora A and B: a single residue change transforms Aurora A into correctly localized and functional Aurora B. Mol Biol Cell. 2009; 20(15):3491-502. PMC: 2719567. DOI: 10.1091/mbc.e09-05-0370. View

15.

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

16.

Wang H, Gottfries J, Barrenas F, Benson M . Identification of novel biomarkers in seasonal allergic rhinitis by combining proteomic, multivariate and pathway analysis. PLoS One. 2011; 6(8):e23563. PMC: 3160968. DOI: 10.1371/journal.pone.0023563. View

17.

Krogan N, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A . Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006; 440(7084):637-43. DOI: 10.1038/nature04670. View

18.

Rao P, Satelli A, Zhang S, Srivastava S, Srivenugopal K, Rao U . RNF2 is the target for phosphorylation by the p38 MAPK and ERK signaling pathways. Proteomics. 2009; 9(10):2776-87. PMC: 2992961. DOI: 10.1002/pmic.200800847. View

19.

Chica C, Diella F, Gibson T . Evidence for the concerted evolution between short linear protein motifs and their flanking regions. PLoS One. 2009; 4(7):e6052. PMC: 2702822. DOI: 10.1371/journal.pone.0006052. View

20.

Fabbro M, Savage K, Hobson K, Deans A, Powell S, McArthur G . BRCA1-BARD1 complexes are required for p53Ser-15 phosphorylation and a G1/S arrest following ionizing radiation-induced DNA damage. J Biol Chem. 2004; 279(30):31251-8. DOI: 10.1074/jbc.M405372200. View