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. 2012 Jun 22;3(7):508–520. doi: 10.1007/s13238-012-2945-1

Proteome-wide prediction of protein-protein interactions from high-throughput data

Zhi-Ping Liu 1,✉, Luonan Chen 1,2,✉
PMCID: PMC4875394  PMID: 22729399

Abstract

In this paper, we present a brief review of the existing computational methods for predicting proteome-wide protein-protein interaction networks from high-throughput data. The availability of various types of omics data provides great opportunity and also unprecedented challenge to infer the interactome in cells. Reconstructing the interactome or interaction network is a crucial step for studying the functional relationship among proteins and the involved biological processes. The protein interaction network will provide valuable resources and alternatives to decipher the mechanisms of these functionally interacting elements as well as the running system of cellular operations. In this paper, we describe the main steps of predicting protein-protein interaction networks and categorize the available approaches to couple the physical and functional linkages. The future topics and the analyses beyond prediction are also discussed and concluded.

Keywords: proteomics, protein-protein interaction, prediction, systems biology

Contributor Information

Zhi-Ping Liu, Email: zpliu@sibs.ac.cn.

Luonan Chen, Email: lnchen@sibs.ac.cn.

References

  1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Andres L.E., Ezkurdia I., Garcia B., Valencia A., Juan D. EcID. A database for the inference of functional interactions in E. coli. Nucleic Acids Res. 2009;37:D629–D635. doi: 10.1093/nar/gkn853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Aranda B., Achuthan P., Alam-Faruque Y., Armean I., Bridge A., Derow C., Feuermann M., Ghanbarian A.T., Kerrien S., Khadake J., et al. The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2010;38:D525–D531. doi: 10.1093/nar/gkp878. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Aytuna A.S., Gursoy A., Keskin O. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics. 2005;21:2850–2855. doi: 10.1093/bioinformatics/bti443. [DOI] [PubMed] [Google Scholar]
  5. Bader G.D., Betel D., Hogue C.W. BIND: the biomolecular interaction network database. Nucleic Acids Res. 2003;31:248–250. doi: 10.1093/nar/gkg056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bader J.S., Chaudhuri A., Rothberg J.M., Chant J. Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol. 2004;22:78–85. doi: 10.1038/nbt924. [DOI] [PubMed] [Google Scholar]
  7. Barabasi A.L., Oltvai Z. Network biology: understanding the cell’s functional organization. Nat Rev Genet. 2004;5:101–113. doi: 10.1038/nrg1272. [DOI] [PubMed] [Google Scholar]
  8. Barrett T., Troup D.B., Wilhite S.E., Ledoux P., Rudnev D., Evangelista C., Kim I.F., Soboleva A., Tomashevsky M., Edgar R. NCBI GEO: mining tens of millions of expression profiles—database and tools update. Nucleic Acids Res. 2007;35:D760–D765. doi: 10.1093/nar/gkl887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Biocarta. (2012). Available: http://cgap.nci.nih.gov/Pathways/BioCarta_Pathways. Accessed April 7, 2012.
  10. Bossi A., Lehner B. Tissue specificity and the human protein interaction network. Mol Syst Biol. 2009;5:260. doi: 10.1038/msb.2009.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Behrends C., Sowa M.E., Gygi S.P., Harper J.W. Network organization of the human autophagy system. Nature. 2010;466:68–76. doi: 10.1038/nature09204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Bhardwaj N., Lu H. Correlation between gene expression profiles and protein-protein interactions within and across genomes. Bioinformatics. 2005;21:2730–2738. doi: 10.1093/bioinformatics/bti398. [DOI] [PubMed] [Google Scholar]
  13. Bork P., Jensen L.J., von Mering C., Ramani A.K., Lee I., Marcotte E.M. Protein interaction networks from yeast to human. Curr Opin Struct Biol. 2004;14:292–299. doi: 10.1016/j.sbi.2004.05.003. [DOI] [PubMed] [Google Scholar]
  14. Brown K.R., Jurisica I. Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol. 2007;8:R95. doi: 10.1186/gb-2007-8-5-r95. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., Thompson J.D. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003;31:3497–3500. doi: 10.1093/nar/gkg500. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Chatr-aryamontri A., Ceol A., Palazzi L.M., Nardelli G., Schneider M.V., Castagnoli L., Cesareni G. MINT: the Molecular INTeraction database. Nucleic Acids Res. 2007;35:D572–D574. doi: 10.1093/nar/gkl950. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Chen L., Liu R., Liu Z.P., Li M., Aihara K. Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers. Sci Rep. 2012;2:342. doi: 10.1038/srep00342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Chen L., Wang R.S., Zhang X.S. Biomolecular networks: methods and applications in systems biology. Hoboken, New Jersey: John Wiley & Sons; 2009. [Google Scholar]
  19. Chen L., Wang R., Li C., Aihara K. Modelling biomolecular networks in cells: structures and dynamics. Berlin: Springer-Verlag; 2010. [Google Scholar]
  20. Chen L., Wu L.Y., Wang Y., Zhang X.S. Inferring protein interactions from experimental data by association probabilistic method. Proteins. 2006;62:833–837. doi: 10.1002/prot.20783. [DOI] [PubMed] [Google Scholar]
  21. Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E., et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393:537–544. doi: 10.1038/31159. [DOI] [PubMed] [Google Scholar]
  22. Dandekar T., Snel B., Huynen M., Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci. 1998;23:324–328. doi: 10.1016/S0968-0004(98)01274-2. [DOI] [PubMed] [Google Scholar]
  23. Enright A.J., Iliopoulos I., Kyrpides N.C., Ouzounis C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature. 1999;402:86–90. doi: 10.1038/47056. [DOI] [PubMed] [Google Scholar]
  24. Eisenberg D., Marcotte E.M., Xenarios I., Yeates T.O. Protein function in the post-genomic era. Nature. 2000;405:823–826. doi: 10.1038/35015694. [DOI] [PubMed] [Google Scholar]
  25. Ge H., Liu Z., Church G.M., Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet. 2001;29:482–486. doi: 10.1038/ng776. [DOI] [PubMed] [Google Scholar]
  26. Gobel U., Sander C., Schneider R., Valencia A. Correlated mutations and residue contacts in proteins. Proteins. 1994;18:309–317. doi: 10.1002/prot.340180402. [DOI] [PubMed] [Google Scholar]
  27. Goh C.S., Bogan A.A., Joachimiak M., Walther D., Cohen F.E. Co-evolution of proteins with their interaction partners. J Mol Biol. 2000;299:283–293. doi: 10.1006/jmbi.2000.3732. [DOI] [PubMed] [Google Scholar]
  28. Goh K.I., Cusick M.E., Valle D., Childs B., Vidal M., Barabasi A.L. The human disease network. Proc Natl Acad Sci U S A. 2007;104:8685–8690. doi: 10.1073/pnas.0701361104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Grigoriev A. A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 2001;29:3513–3519. doi: 10.1093/nar/29.17.3513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Guo Y., Yu L., Wen Z., Li M. Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. Nucleic Acids Res. 2008;36:3025–3030. doi: 10.1093/nar/gkn159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Han J.D., Bertin N., Hao T., Goldberg D.S., Berriz G.F., Zhang L.V., Dupuy D., Walhout A.J., Cusick M.E., Roth F.P., et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature. 2004;430:88–93. doi: 10.1038/nature02555. [DOI] [PubMed] [Google Scholar]
  32. Han K., Park B., Kim H., Hong J., Park J. PID: the Human Protein Interaction Database. Bioinformatics. 2004;20:2466–2470. doi: 10.1093/bioinformatics/bth253. [DOI] [PubMed] [Google Scholar]
  33. Hayashida M., Ueda N., Akutsu T. Inferring strengths of protein-protein interactions from experimental data using linear programming. Bioinformatics. 2003;19:ii58–ii65. doi: 10.1093/bioinformatics/btg1061. [DOI] [PubMed] [Google Scholar]
  34. He D., Liu Z.P., Chen L. Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. BMC Genomics. 2011;12:592. doi: 10.1186/1471-2164-12-592. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. He D., Liu Z.P., Honda M., Kaneko S., Chen L. Coexpression network analysis in chronic hepatitis B and C hepatic lesion reveals distinct patterns of disease progression to hepatocellular carcinoma. J Mol Cell Biol. 2012;4:140–152. doi: 10.1093/jmcb/mjs011. [DOI] [PubMed] [Google Scholar]
  36. Huynen M., Snel B., Lathe W., 3rd, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 2000;10:1204–1210. doi: 10.1101/gr.10.8.1204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Ideker T., Sharan R. Protein networks in disease. Genome Res. 2008;18:644–652. doi: 10.1101/gr.071852.107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Jager S., Cimermancic P., Gulbahce N., Johnson J.R., McGovern K.E., Clarke S.C., Shales M., Mercenne G., Pache L., Li K., et al. Global landscape of HIV-human protein complexes. Nature. 2011;481:365–370. doi: 10.1038/nature10719. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Jansen R., Greenbaum D., Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Res. 2002;12:37–46. doi: 10.1101/gr.205602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Jansen R., Yu H., Greenbaum D., Kluger Y., Krogan N.J., Chung S., Emili A., Snyder M., Greenblatt J.F., Gerstein M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003;302:449–453. doi: 10.1126/science.1087361. [DOI] [PubMed] [Google Scholar]
  41. Jothi R., Kann M.G., Przytycka T.M. Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics. 2005;21:i241–i250. doi: 10.1093/bioinformatics/bti1009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Kanehisa M., Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30. doi: 10.1093/nar/28.1.27. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Kerrien S., Alam-Faruque Y., Aranda B., Bancarz I., Bridge A., Derow C., Dimmer E., Feuermann M., Friedrichsen A., Huntley R., et al. IntAct—open source resource for molecular interaction data. Nucleic Acids Res. 2007;35:D561–D565. doi: 10.1093/nar/gkl958. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Lage K., Mollgard K., Greenway S., Wakimoto H., Gorham J.M., Workman C.T., Bendsen E., Hansen N.T., Rigina O., Roque F.S., et al. Dissecting spatio-temporal protein networks driving human heart development and related disorders. Mol Syst Biol. 2010;6:381. doi: 10.1038/msb.2010.36. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Lee K., Chuang H.Y., Beyer A., Sung M.K., Huh W.K., Lee B., Ideker T. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res. 2008;36:e136. doi: 10.1093/nar/gkn619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Liu X., Liu Z.P., Zhao X.M., Chen L. Identifying disease genes and module biomarkers with differential interactions. J Am Med Inform Assoc. 2012;19:241–248. doi: 10.1136/amiajnl-2011-000658. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Liu Z.P., Wang J., Qiu Y.Q., Leung R.K.K., Zhang X.S., Tsui S.T.W., Chen L. Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. BMC Bioinformatics. 2012;13(Suppl7):S6. doi: 10.1186/1471-2105-13-S7-S6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Liu Z.P., Wang Y., Zhang X.S., Chen L. Network-based analysis of complex diseases. IET Syst Biol. 2012;6:22–33. doi: 10.1049/iet-syb.2010.0052. [DOI] [PubMed] [Google Scholar]
  49. Liu Z.P., Wang Y., Zhang X.S., Xia W., Chen L. Detecting and analyzing differentially activated pathways in brain regions of Alzheimer’s disease patients. Mol Biosyst. 2011;7:1441–1452. doi: 10.1039/c0mb00325e. [DOI] [PubMed] [Google Scholar]
  50. Liu Z.P., Wu L.Y., Wang Y., Chen L., Zhang X.S. Predicting gene ontology functions from protein’s regional surface structures. BMC Bioinformatics. 2007;8:475. doi: 10.1186/1471-2105-8-475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Liu Z.P., Wu L.Y., Wang Y., Zhang X.S., Chen L. Prediction of protein-RNA binding sites by a random forest method with combined features. Bioinformatics. 2010;26:1616–1622. doi: 10.1093/bioinformatics/btq253. [DOI] [PubMed] [Google Scholar]
  52. Lu L.J., Xia Y., Paccanaro A., Yu H., Gerstein M. Assessing the limits of genomic data integration for predicting protein networks. Genome Res. 2005;15:945–953. doi: 10.1101/gr.3610305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. von Mering C., Jensen L.J., Kuhn M., Chaffron S., Doerks T., Kruger B., Snel B., Bork P. STRING 7 — recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 2007;35:D358–D362. doi: 10.1093/nar/gkl825. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., Alon U. Network motifs: simple building blocks of complex networks. Science. 2002;298:824–827. doi: 10.1126/science.298.5594.824. [DOI] [PubMed] [Google Scholar]
  55. Newman M.E., Girvan M. Finding and evaluating community structure in networks. Phys Rev E. 2004;69:026113. doi: 10.1103/PhysRevE.69.026113. [DOI] [PubMed] [Google Scholar]
  56. Overbeek R., Fonstein M., D’souza M., Pusch G.D., Maltsev N. Use of contiguity on the chromosome to predict functional coupling. In Silico Biol. 1999;1:93–108. [PubMed] [Google Scholar]
  57. Pagel P., Kovac S., Oesterheld M., Brauner B., Dunger-Kaltenbach I., Frishman G., Montrone C., Mark P., Stumpflen V., Mewes H.W., et al. The MIPS mammalian proteinprotein interaction database. Bioinformatics. 2005;21:832–834. doi: 10.1093/bioinformatics/bti115. [DOI] [PubMed] [Google Scholar]
  58. Pazos F., Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 2001;14:609–614. doi: 10.1093/protein/14.9.609. [DOI] [PubMed] [Google Scholar]
  59. Pazos F., Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins. 2002;47:219–227. doi: 10.1002/prot.10074. [DOI] [PubMed] [Google Scholar]
  60. Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., Yeates T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A. 1999;96:4285–4288. doi: 10.1073/pnas.96.8.4285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Prasad T.S.K., Goel R., Kandasamy K., Keerthikumar S., Kumar S., Mathivanan S., Telikicherla D., Raju R., et al. Human Protein Reference Database — 2009 update. Nucleic Acids Res. 2009;37:D767–D772. doi: 10.1093/nar/gkn892. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Shen J., Zhang J., Luo X., Zhu W., Yu K., Chen K., Li Y., Jiang H. Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci U S A. 2007;104:4337–4341. doi: 10.1073/pnas.0607879104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Skrabanek L., Saini H.K., Bader G.D., Enright A.J. Computational prediction of protein-protein interactions. Mol Biotechnol. 2008;38:1–17. doi: 10.1007/s12033-007-0069-2. [DOI] [PubMed] [Google Scholar]
  64. Smith G.R., Sternberg M.J. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol. 2002;12:28–35. doi: 10.1016/S0959-440X(02)00285-3. [DOI] [PubMed] [Google Scholar]
  65. Sprinzak E., Margalit H. Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol. 2001;311:681–692. doi: 10.1006/jmbi.2001.4920. [DOI] [PubMed] [Google Scholar]
  66. Stark C., Breitkreutz B.J., Reguly T., Boucher L., Breitkreutz A., Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006;34:D535–D539. doi: 10.1093/nar/gkj109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Szilagyi A., Grimm V., Arakaki A.K., Skolnick J. Prediction of physical protein-protein interactions. Phys Biol. 2005;2:S1–S16. doi: 10.1088/1478-3975/2/2/S01. [DOI] [PubMed] [Google Scholar]
  68. Tamames J., Casari G., Ouzounis C., Valencia A. Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol. 1997;44:66–73. doi: 10.1007/PL00006122. [DOI] [PubMed] [Google Scholar]
  69. Tsoka S., Ouzounis C.A. Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nat Genet. 2000;26:141–142. doi: 10.1038/79847. [DOI] [PubMed] [Google Scholar]
  70. Sapkota A., Liu X., Zhao X.M., Cao Y., Liu J., Liu Z.P., Chen L. DIPOS: database of interacting proteins in Oryza sativa. Mol Biosyst. 2011;7:2615–2621. doi: 10.1039/c1mb05120b. [DOI] [PubMed] [Google Scholar]
  71. Salwinski L., Miller C.S., Smith A.J., Pettit F.K., Bowie J.U., Eisenberg D. The database of interacting proteins: 2004 update. Nucleic Acids Res. 2004;32:D449–D451. doi: 10.1093/nar/gkh086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  72. Smialowski P., Pagel P., Wong P., Brauner B., Dunger I., Fobo G., Frishman G., Montrone C., Rattei T., Frishman D., et al. The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res. 2009;38:D540–D544. doi: 10.1093/nar/gkp1026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  73. Valencia A., Pazos F. Computational methods for the prediction of protein interactions. Curr Opin Struct Biol. 2002;12:368–373. doi: 10.1016/S0959-440X(02)00333-0. [DOI] [PubMed] [Google Scholar]
  74. Vapnik V. The nature of statistical learning theory. New York: Springer-Verlag; 1995. [Google Scholar]
  75. Vastrik I., D’Eustachio P., Schmidt E., Joshi-Tope G., Gopinath G., Croft D., de Bono B., Gillespie M., Jassal B., Lewis S., et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 2007;8:R39. doi: 10.1186/gb-2007-8-3-r39. [DOI] [PMC free article] [PubMed] [Google Scholar]
  76. Walhout A.J., Sordella R., Lu X., Hartley J.L., Temple G.F., Brasch M.A., Thierry-Mieg N., Vidal M. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science. 2000;287:116–122. doi: 10.1126/science.287.5450.116. [DOI] [PubMed] [Google Scholar]
  77. Wang R.S., Wang Y., Wu L.Y., Zhang X.S., Chen L. Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformatics. 2007;8:391. doi: 10.1186/1471-2105-8-391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  78. Wang J., Huo K., Ma L., Tang L., Li D., Huang X., Yuan Y., Li C., Wang W., Guan W., et al. Toward an understanding of the protein interaction network of the human liver. Mol Syst Biol. 2011;7:536. doi: 10.1038/msb.2011.67. [DOI] [PMC free article] [PubMed] [Google Scholar]
  79. Wang L., Liu Z.P., Zhang X.S., Chen L. Prediction of hot spots in protein interfaces using a random forest model with hybrid features. Protein Eng Des Sel. 2012;25:119–126. doi: 10.1093/protein/gzr066. [DOI] [PubMed] [Google Scholar]
  80. Winter C., Henschel A., Kim W.K., Schroeder M. SCOPPI: a structural classification of protein-protein interfaces. Nucleic Acids Res. 2006;34:D310–D314. doi: 10.1093/nar/gkj099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  81. Wu J., Kasif S., DeLisi C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics. 2003;19:1524–1530. doi: 10.1093/bioinformatics/btg187. [DOI] [PubMed] [Google Scholar]
  82. Yu H., Luscombe N.M., Lu H.X., Zhu X., Xia Y., Han J.D., Bertin N., Chung S., Vidal M., Gerstein M. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 2004;14:1107–1118. doi: 10.1101/gr.1774904. [DOI] [PMC free article] [PubMed] [Google Scholar]
  83. Yu X., Wallqvist A., Reifman J. Inferring high-confidence human protein-protein interactions. BMC Bioinformatics. 2012;13:79. doi: 10.1186/1471-2105-13-79. [DOI] [PMC free article] [PubMed] [Google Scholar]
  84. Zhang X.S., Wang R.S., Wang Y., Wang J., Qiu Y., Wang L., Chen L. Modularity optimization in community detection of complex networks. Europhys Lett. 2009;87:38002. doi: 10.1209/0295-5075/87/38002. [DOI] [Google Scholar]
  85. Zhao X.M., Chen L., Aihara K. A discriminative approach to identifying domain-domain interactions from protein-protein interactions. Proteins. 2010;78:1243–1253. doi: 10.1002/prot.22643. [DOI] [PubMed] [Google Scholar]
  86. Zhao X.M., Zhang X.W., Tang W., Chen L. FPPI: Fusarium graminearum protein-protein interaction database. J Proteome Res. 2009;8:4714–4721. doi: 10.1021/pr900415b. [DOI] [PubMed] [Google Scholar]
  87. Zhou H.X., Shan Y. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins. 2001;44:336–343. doi: 10.1002/prot.1099. [DOI] [PubMed] [Google Scholar]

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