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Volumn 11, Issue 18, 2014, Pages 22-27

The role of protein interaction networks in systems biomedicine

Author keywords

Disease genes; Gene expression; Human diseases; Interactome; Network

Indexed keywords


EID: 84923201396     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.1016/j.csbj.2014.08.008     Document Type: Review
Times cited : (106)

References (66)
  • 1
    • 0001194208 scopus 로고
    • Genetic control of biochemical reactions, in Neurospora
    • G.W. Beadle, and E.L. Tatum Genetic control of biochemical reactions, in Neurospora Proc Natl Acad Sci U S A 27 1941 499 506
    • (1941) Proc Natl Acad Sci U S A , vol.27 , pp. 499-506
    • Beadle, G.W.1    Tatum, E.L.2
  • 2
    • 84884494841 scopus 로고    scopus 로고
    • The protein-protein interaction network of the human Sirtuin family
    • A. Sharma, S. Costantini, and G. Colonn The protein-protein interaction network of the human Sirtuin family Biochim Biophys Acta 1834 2013 1998 2009
    • (2013) Biochim Biophys Acta , vol.1834 , pp. 1998-2009
    • Sharma, A.1    Costantini, S.2    Colonn, G.3
  • 3
    • 0036013593 scopus 로고    scopus 로고
    • Statistical mechanics of complex networks
    • R. Albert, and A.L. Barabasi Statistical mechanics of complex networks Rev Mod Phys 74 2002 47 97
    • (2002) Rev Mod Phys , vol.74 , pp. 47-97
    • Albert, R.1    Barabasi, A.L.2
  • 4
    • 84902547630 scopus 로고    scopus 로고
    • An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods
    • G. Valentini, A. Paccanaro, H. Caniza, A.E. Romero, and R. Matteo An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods Artif Intell Med 2014 10.1016/j.artmed.2014.03.003
    • (2014) Artif Intell Med
    • Valentini, G.1    Paccanaro, A.2    Caniza, H.3    Romero, A.E.4    Matteo, R.5
  • 5
    • 34547566679 scopus 로고    scopus 로고
    • Understanding signaling in yeast: Insights from network analysis
    • K.Y. Arga, Z.I. Önsan, B. KIrdar, K.Ö. Ülgen, and J. Nielsen Understanding signaling in yeast: insights from network analysis Biotechnol Bioeng 97 5 2007 1246 1258 10.1002/bit.21317
    • (2007) Biotechnol Bioeng , vol.97 , Issue.5 , pp. 1246-1258
    • Arga, K.Y.1    Önsan, Z.I.2    Kirdar, B.3    Ülgen, K.O.4    Nielsen, J.5
  • 6
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • R. Sharan, I. Ulitsky, and R. Shamir Network-based prediction of protein function Mol Syst Biol 3 2007 88
    • (2007) Mol Syst Biol , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 7
    • 84875276463 scopus 로고    scopus 로고
    • A fast ranking algorithm for predicting gene functions in biomolecular networks
    • M. Re, M. Mesiti, and G. Valentini A fast ranking algorithm for predicting gene functions in biomolecular networks IEEE ACM Trans Comput Biol Bioinf 9 6 2012 1812 1818
    • (2012) IEEE ACM Trans Comput Biol Bioinf , vol.9 , Issue.6 , pp. 1812-1818
    • Re, M.1    Mesiti, M.2    Valentini, G.3
  • 8
    • 47549107689 scopus 로고    scopus 로고
    • GeneMANIA: A real-time multiple association network integration algorithm for predicting gene function
    • S. Mostafavi, D. Ray, D. Warde-Farley, C. Grouios, and Q. Morris GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function Genome Biol 9 S4 2008
    • (2008) Genome Biol , vol.9 , Issue.S4
    • Mostafavi, S.1    Ray, D.2    Warde-Farley, D.3    Grouios, C.4    Morris, Q.5
  • 9
    • 84928393479 scopus 로고    scopus 로고
    • Think globally and solve locally: Secondary memory-based network learning for automated multi-species function prediction
    • M. Mesiti, M. Re, and G. Valentini Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction GigaScience 3 2014 5
    • (2014) GigaScience , vol.3 , pp. 5
    • Mesiti, M.1    Re, M.2    Valentini, G.3
  • 10
    • 67349200229 scopus 로고    scopus 로고
    • Interaction networks: From protein functions to drug discovery: A review
    • E. Chautard, N. Thierry-Mieg, and S. Ricard-Blum Interaction networks: from protein functions to drug discovery: a review Pathol Biol 57 2009 324 333
    • (2009) Pathol Biol , vol.57 , pp. 324-333
    • Chautard, E.1    Thierry-Mieg, N.2    Ricard-Blum, S.3
  • 12
    • 63449132586 scopus 로고    scopus 로고
    • Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks
    • X. Yang, J.L. Deignan, H. Qi, J. Zhu, S. Qian, and G. Torosyan Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks Nat Genet 41 2009 415 423
    • (2009) Nat Genet , vol.41 , pp. 415-423
    • Yang, X.1    Deignan, J.L.2    Qi, H.3    Zhu, J.4    Qian, S.5    Torosyan, G.6
  • 16
    • 84863677563 scopus 로고    scopus 로고
    • Google goes cancer: Improving outcome prediction for cancer patients by network-based ranking of marker genes
    • C. Winter, G. Kristiansen, S. Kersting, J. Roy, D. Aust, and T. Knösel Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes PLoS Comput Biol 8 5 2012
    • (2012) PLoS Comput Biol , vol.8 , Issue.5
    • Winter, C.1    Kristiansen, G.2    Kersting, S.3    Roy, J.4    Aust, D.5    Knösel, T.6
  • 17
    • 79958754253 scopus 로고    scopus 로고
    • PREDICT, a method for inferring novel drug indications with application to personalized medicine
    • A. Gottlieb, G.Y. Stein, E. Ruppin, and R. Sharan PREDICT, a method for inferring novel drug indications with application to personalized medicine Mol Syst Biol 7 2011 496
    • (2011) Mol Syst Biol , vol.7 , pp. 496
    • Gottlieb, A.1    Stein, G.Y.2    Ruppin, E.3    Sharan, R.4
  • 19
    • 84894539685 scopus 로고    scopus 로고
    • Network-based drug ranking and repositioning with respect to DrugBank therapeutic categories
    • M. Re, and G. Valentini Network-based drug ranking and repositioning with respect to DrugBank therapeutic categories IEEE ACM Trans Comput Biol Bioinf 10 6 2013 1359 1371
    • (2013) IEEE ACM Trans Comput Biol Bioinf , vol.10 , Issue.6 , pp. 1359-1371
    • Re, M.1    Valentini, G.2
  • 20
    • 33751356890 scopus 로고    scopus 로고
    • BNArray: An R package for constructing gene regulatory networks from microarray data by using Bayesian network
    • X. Chen, M. Chen, and K. Ning BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network Bioinformatics 22 2006 2952 2954
    • (2006) Bioinformatics , vol.22 , pp. 2952-2954
    • Chen, X.1    Chen, M.2    Ning, K.3
  • 21
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: An R package for weighted correlation network analysis
    • P. Langfelder, and S. Horvath WGCNA: an R package for weighted correlation network analysis BMC Bioinformatics 9 2008 559
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 23
    • 49549092691 scopus 로고    scopus 로고
    • Protein-protein interactions: From global to local analyses
    • W.P. Kelly, and M.P.H. Stumpf Protein-protein interactions: from global to local analyses Curr Opin Biotechnol 19 2008 396 403
    • (2008) Curr Opin Biotechnol , vol.19 , pp. 396-403
    • Kelly, W.P.1    Stumpf, M.P.H.2
  • 24
    • 84875275699 scopus 로고    scopus 로고
    • Human diseases through the lens of network biology
    • L. Furlong Human diseases through the lens of network biology Trends Genet 29 2013 3
    • (2013) Trends Genet , vol.29 , pp. 3
    • Furlong, L.1
  • 27
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • S. Fields, and O. Song A novel genetic system to detect protein-protein interactions Nature 340 6230 1989 245 246
    • (1989) Nature , vol.340 , Issue.6230 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 28
    • 0032828715 scopus 로고    scopus 로고
    • A generic protein purification method for protein complex characterization and proteome exploration
    • G. Rigaut, A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin A generic protein purification method for protein complex characterization and proteome exploration Nat Biotechnol 10 1999 1030 1032
    • (1999) Nat Biotechnol , vol.10 , pp. 1030-1032
    • Rigaut, G.1    Shevchenko, A.2    Rutz, B.3    Wilm, M.4    Mann, M.5    Seraphin, B.6
  • 29
    • 77958498250 scopus 로고    scopus 로고
    • Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data
    • Z.-H. You, Y.-K. Lei, J. Gui, D.-S. Huang, and X. Zhou Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data Bioinformatics 26 21 2010 2744 2751 10.1093/bioinformatics/btq510
    • (2010) Bioinformatics , vol.26 , Issue.21 , pp. 2744-2751
    • You, Z.-H.1    Lei, Y.-K.2    Gui, J.3    Huang, D.-S.4    Zhou, X.5
  • 30
    • 0037432528 scopus 로고    scopus 로고
    • How reliable are experimental protein-protein interaction data?
    • E. Sprinzak, S. Sattath, and H. Margalit How reliable are experimental protein-protein interaction data? J Mol Biol 327 2003 919 923
    • (2003) J Mol Biol , vol.327 , pp. 919-923
    • Sprinzak, E.1    Sattath, S.2    Margalit, H.3
  • 31
    • 33745619564 scopus 로고    scopus 로고
    • Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
    • H.N. Chua, W.-K. Sung, and L. Wong Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions Bioinformatics 22 2006 1623 1630
    • (2006) Bioinformatics , vol.22 , pp. 1623-1630
    • Chua, H.N.1    Sung, W.-K.2    Wong, L.3
  • 32
    • 0036580169 scopus 로고    scopus 로고
    • Protein interactions: Two methods for assessment of the reliability of high throughput observations
    • C.M. Deane, Ł. Salwiński, I. Xenarios, and D. Eisenberg Protein interactions: two methods for assessment of the reliability of high throughput observations Mol Cell Proteomics 1 5 2002 349 356
    • (2002) Mol Cell Proteomics , vol.1 , Issue.5 , pp. 349-356
    • Deane, C.M.1    Salwiński Ł.2    Xenarios, I.3    Eisenberg, D.4
  • 33
    • 33845450589 scopus 로고    scopus 로고
    • Mining literature for systems biology
    • P.M. Roberts Mining literature for systems biology Brief Bioinform 7 2006 399 406
    • (2006) Brief Bioinform , vol.7 , pp. 399-406
    • Roberts, P.M.1
  • 34
    • 0035755746 scopus 로고    scopus 로고
    • Exploiting big biology: Integrating large-scale biological data for functional inference
    • E.M. Marcotte, and S.V. Date Exploiting big biology: integrating large-scale biological data for functional inference Brief Bioinform 2 4 2001 363 374
    • (2001) Brief Bioinform , vol.2 , Issue.4 , pp. 363-374
    • Marcotte, E.M.1    Date, S.V.2
  • 35
    • 0035222942 scopus 로고    scopus 로고
    • Protein interaction maps for model organisms
    • A.J. Walhout, and M. Vidal Protein interaction maps for model organisms Nat Rev Mol Cell Biol 2 2001 55 62
    • (2001) Nat Rev Mol Cell Biol , vol.2 , pp. 55-62
    • Walhout, A.J.1    Vidal, M.2
  • 36
    • 79959264888 scopus 로고    scopus 로고
    • A novel integrative network approach to understand the interplay between cardiovascular disease and other complex disorders
    • D. Rende, N. Baysal, and B. Kirdar A novel integrative network approach to understand the interplay between cardiovascular disease and other complex disorders Mol Biosyst 7 2011 2205 2219 10.1039/c1mb05064h
    • (2011) Mol Biosyst , vol.7 , pp. 2205-2219
    • Rende, D.1    Baysal, N.2    Kirdar, B.3
  • 37
    • 84878896486 scopus 로고    scopus 로고
    • Complex disease interventions from a network model for type 2 diabetes
    • D. Rende, N. Baysal, and B. Kirdar Complex disease interventions from a network model for type 2 diabetes PLoS ONE 2013 10.1371/journal.pone.0065854
    • (2013) PLoS ONE
    • Rende, D.1    Baysal, N.2    Kirdar, B.3
  • 38
    • 84934441103 scopus 로고    scopus 로고
    • Computational approaches for human disease gene prediction and ranking
    • C. Zhu, C. Wu, B.J. Aronow, and A.G. Jegga Computational approaches for human disease gene prediction and ranking Adv Exp Med Biol 799 2014 69 84
    • (2014) Adv Exp Med Biol , vol.799 , pp. 69-84
    • Zhu, C.1    Wu, C.2    Aronow, B.J.3    Jegga, A.G.4
  • 41
    • 79952674000 scopus 로고    scopus 로고
    • Interactome networks and human disease
    • M. Vidal, M.E. Cusick, and A.-L. Barabasi Interactome networks and human disease Cell 144 2011 986 998
    • (2011) Cell , vol.144 , pp. 986-998
    • Vidal, M.1    Cusick, M.E.2    Barabasi, A.-L.3
  • 43
    • 53349117774 scopus 로고    scopus 로고
    • High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
    • H. Yu, P. Braun, M.A. YIldIrIm, I. Lemmens, K. Venkatesan, and J. Sahalie High-Quality Binary Protein Interaction Map of the Yeast Interactome Network Science 322 5898 2008 104 110
    • (2008) Science , vol.322 , Issue.5898 , pp. 104-110
    • Yu, H.1    Braun, P.2    Yildirim, M.A.3    Lemmens, I.4    Venkatesan, K.5    Sahalie, J.6
  • 44
    • 33846672214 scopus 로고    scopus 로고
    • Biological network comparison using graphlet degree distribution
    • N. Przulj Biological network comparison using graphlet degree distribution Bioinformatics 23 2007 177 183
    • (2007) Bioinformatics , vol.23 , pp. 177-183
    • Przulj, N.1
  • 45
    • 12344273375 scopus 로고    scopus 로고
    • Modeling interactome: Scale-free or geometric?
    • N. Przulj, D.G. Corneil, and I. Jurisica Modeling interactome: scale-free or geometric? Bioinformatics 20 2004 3508 3515
    • (2004) Bioinformatics , vol.20 , pp. 3508-3515
    • Przulj, N.1    Corneil, D.G.2    Jurisica, I.3
  • 46
    • 84874289423 scopus 로고    scopus 로고
    • Graphlet-based measures are suitable for biological network comparison
    • W. Hayes, K. Sun, and N. Przulj Graphlet-based measures are suitable for biological network comparison Bioinformatics 29 4 2013 483 491
    • (2013) Bioinformatics , vol.29 , Issue.4 , pp. 483-491
    • Hayes, W.1    Sun, K.2    Przulj, N.3
  • 47
    • 79952635505 scopus 로고    scopus 로고
    • Principles and strategies for developing network models in cancer
    • D. Pe'er, and N. Hacohen Principles and strategies for developing network models in cancer Cell 144 2011 864 873
    • (2011) Cell , vol.144 , pp. 864-873
    • Pe'Er, D.1    Hacohen, N.2
  • 48
    • 44949142848 scopus 로고    scopus 로고
    • Evolution and dynamics of protein interactions and Networks
    • E.D. Levy, and J.B. Pereira-Leal Evolution and dynamics of protein interactions and Networks Curr Opin Struct Biol 18 2008 349 357
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 349-357
    • Levy, E.D.1    Pereira-Leal, J.B.2
  • 49
    • 62049085339 scopus 로고    scopus 로고
    • Drug targets for tumorigenesis: Insights from structural analysis of EGFR signaling network
    • S.D. Tekir, K.Y. Arga, and K.Ö. Ülgen Drug targets for tumorigenesis: insights from structural analysis of EGFR signaling network J Biomed Inform 42 2009 228 236 10.1016/j.jbi.2008.08.008
    • (2009) J Biomed Inform , vol.42 , pp. 228-236
    • Tekir, S.D.1    Arga, K.Y.2    Ülgen, K.O.3
  • 50
    • 67349276056 scopus 로고    scopus 로고
    • A network medicine approach to human disease
    • A. Zanzoni, M. Soler-López, and P. Aloy A network medicine approach to human disease FEBS Lett 583 2009 1759 1765
    • (2009) FEBS Lett , vol.583 , pp. 1759-1765
    • Zanzoni, A.1    Soler-López, M.2    Aloy, P.3
  • 51
    • 33845545435 scopus 로고    scopus 로고
    • The modular nature of genetic diseases
    • M. Oti, and H.G. Brunner The modular nature of genetic diseases Clin Genet 71 2007 1 11
    • (2007) Clin Genet , vol.71 , pp. 1-11
    • Oti, M.1    Brunner, H.G.2
  • 52
    • 84891888035 scopus 로고    scopus 로고
    • Analysis of human genes with protein-protein interaction network for detecting disease genes
    • S-Y Wu, F-J Shaoa, R-C Sun, Y. Sui, Y. Wang, and J-L. Wang Analysis of human genes with protein-protein interaction network for detecting disease genes Physica A 398 2014 217 228
    • (2014) Physica A , vol.398 , pp. 217-228
    • Wu, S.-Y.1    Shaoa, F.-J.2    Sun, R.-C.3    Sui, Y.4    Wang, Y.5    Wang, J.-L.6
  • 53
    • 83555177301 scopus 로고    scopus 로고
    • Detecting disease genes based on semi-supervised learning and protein-protein interaction networks
    • T.P. Nguyen, and T.B. Ho Detecting disease genes based on semi-supervised learning and protein-protein interaction networks Artif Intell Med 54 2012 63 71
    • (2012) Artif Intell Med , vol.54 , pp. 63-71
    • Nguyen, T.P.1    Ho, T.B.2
  • 54
    • 33646884801 scopus 로고    scopus 로고
    • Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes
    • L. Franke, H. van Bakel, L. Fokkens, E.D. de Jong, M. Egmont-Petersen, and C. Wijmenga Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes Am J Hum Genet 78 2006
    • (2006) Am J Hum Genet , vol.78
    • Franke, L.1    Van Bakel, H.2    Fokkens, L.3    De Jong, E.D.4    Egmont-Petersen, M.5    Wijmenga, C.6
  • 55
    • 41549139527 scopus 로고    scopus 로고
    • Walking the interactome for prioritization of candidate disease genes
    • S. Köhler, S. Bauer, D. Horn, and P.N. Robinson Walking the interactome for prioritization of candidate disease genes Am J Hum Genet 82 2008 949 958
    • (2008) Am J Hum Genet , vol.82 , pp. 949-958
    • Köhler, S.1    Bauer, S.2    Horn, D.3    Robinson, P.N.4
  • 56
    • 77956497662 scopus 로고    scopus 로고
    • Improving disease gene prioritization using the semantic similarity of gene ontology terms
    • A. Schlicker, T. Lengauer, and M. Albrecht Improving disease gene prioritization using the semantic similarity of gene ontology terms Bioinformatics 26 18 2010 561 567
    • (2010) Bioinformatics , vol.26 , Issue.18 , pp. 561-567
    • Schlicker, A.1    Lengauer, T.2    Albrecht, M.3
  • 57
    • 79959898376 scopus 로고    scopus 로고
    • Prioritizing candidate disease genes by network-based boosting of genome-wide association data
    • I. Lee, U. Blom, P. Wang, J. Shim, and E. Marcotte Prioritizing candidate disease genes by network-based boosting of genome-wide association data Genome Res 21 2011 1109 1121
    • (2011) Genome Res , vol.21 , pp. 1109-1121
    • Lee, I.1    Blom, U.2    Wang, P.3    Shim, J.4    Marcotte, E.5
  • 58
    • 84870859088 scopus 로고    scopus 로고
    • Cancer module genes ranking using kernelized score functions
    • M. Re, and G. Valentini Cancer module genes ranking using kernelized score functions BMC Bioinformatics 13 S14 2012 S3
    • (2012) BMC Bioinformatics , vol.13 , Issue.S14 , pp. S3
    • Re, M.1    Valentini, G.2
  • 60
    • 77951952127 scopus 로고    scopus 로고
    • The power of protein interaction networks for associating genes with diseases
    • S. Navlakha, and C. Kingsford The power of protein interaction networks for associating genes with diseases Bioinformatics 26 8 2010 1057 1063
    • (2010) Bioinformatics , vol.26 , Issue.8 , pp. 1057-1063
    • Navlakha, S.1    Kingsford, C.2
  • 61
    • 84876575373 scopus 로고    scopus 로고
    • Assessment of high-confidence protein-protein interactome in yeast
    • K. Karagöz, and K.Y. Arga Assessment of high-confidence protein-protein interactome in yeast J Comput Biol Chem 45 2013 1 8 10.1016/j.compbiolchem.2013.03.002
    • (2013) J Comput Biol Chem , vol.45 , pp. 1-8
    • Karagöz, K.1    Arga, K.Y.2
  • 62
    • 48149084438 scopus 로고    scopus 로고
    • Increasing the reliability of protein interactomes
    • H.N. Chua, and L. Wong Increasing the reliability of protein interactomes Drug Discov Today 13 2008 15 16
    • (2008) Drug Discov Today , vol.13 , pp. 15-16
    • Chua, H.N.1    Wong, L.2
  • 63
    • 34548024598 scopus 로고    scopus 로고
    • Integrating physical and genetic maps: From genomes to interaction networks
    • A. Beyer, S. Bandyopadhyay, and T. Ideker Integrating physical and genetic maps: from genomes to interaction networks Nat. Rev. Genet. 8 2007 699 710
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 699-710
    • Beyer, A.1    Bandyopadhyay, S.2    Ideker, T.3
  • 64
    • 84895471419 scopus 로고    scopus 로고
    • Structural network analysis of biological networks for assessment of potential disease model organisms
    • A.R. Nabhan, and I.N. Sarkar Structural network analysis of biological networks for assessment of potential disease model organisms J Biomed Inform 47 2014 178 191
    • (2014) J Biomed Inform , vol.47 , pp. 178-191
    • Nabhan, A.R.1    Sarkar, I.N.2
  • 65
  • 66
    • 84885393730 scopus 로고    scopus 로고
    • PhenoDigm: Analyzing curated annotations to associate animal models with human diseases
    • [Article ID bat025]
    • D. Smedley, A. Oellrich, S. Kohler, Barbara Ruef, Sanger Mouse Genetics Project, and M. Westerfield PhenoDigm: analyzing curated annotations to associate animal models with human diseases Database 2013 2013 [Article ID bat025]
    • (2013) Database , vol.2013
    • Smedley, D.1    Oellrich, A.2    Kohler, S.3    Ruef, B.4    Mouse Genetics Project, S.5    Westerfield, M.6


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