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Volumn 15, Issue 3, 2018, Pages 850-860

BRANE Clust: Cluster-Assisted Gene Regulatory Network Inference Refinement

Author keywords

clustering; combinatorial optimization; DREAM challenge; Gene regulatory network; transcriptomic data

Indexed keywords

COMBINATORIAL OPTIMIZATION; DATABASE SYSTEMS; ESCHERICHIA COLI; GRAPHIC METHODS; INFORMATION THEORY; LABELING; MATRIX ALGEBRA; MERGING; OPTIMIZATION; PROBABILISTIC LOGICS;

EID: 85046089495     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2017.2688355     Document Type: Article
Times cited : (19)

References (42)
  • 1
    • 67049098922 scopus 로고    scopus 로고
    • Hypergraphs and cellular networks
    • S. Klamt, U.-U. Haus, and F. Theis, "Hypergraphs and cellular networks, " PLoS Comput. Biol., vol. 5, no. 5, 2009. [Online]. Available: http://dx. doi. org/10. 1371/journal. pcbi. 1000385
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.5
    • Klamt, S.1    Haus, U.-U.2    Theis, F.3
  • 2
    • 84962205036 scopus 로고    scopus 로고
    • Flexible data integration and curation using a graph-based approach
    • S. Croset, J. Rupp, and M. Romacker, "Flexible data integration and curation using a graph-based approach, " Bioinf., vol. 32, no. 6, pp. 918-925, 2016. [Online]. Available: http://dx. doi. org/ 10. 1093/bioinformatics/btv644
    • (2016) Bioinf. , vol.32 , Issue.6 , pp. 918-925
    • Croset, S.1    Rupp, J.2    Romacker, M.3
  • 3
    • 84992406259 scopus 로고    scopus 로고
    • APPAGATO: An APproximate PArallel and stochastic GrAph querying TOol for biological networks
    • V. Bonnici, F. Busato, G. Micale, N. Bombieri, A. Pulvirenti, and R. Giugno, "APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks, " Bioinf., vol. 32, no. 14, pp. 2159-2166, 2016. [Online]. Available: http://dx. doi. org/10. 1093/bioinformatics/btw223
    • (2016) Bioinf. , vol.32 , Issue.14 , pp. 2159-2166
    • Bonnici, V.1    Busato, F.2    Micale, G.3    Bombieri, N.4    Pulvirenti, A.5    Giugno, R.6
  • 4
    • 84992417447 scopus 로고    scopus 로고
    • Spectral identification of topological domains
    • J. Chen, A. O. Hero, and I. Rajapakse, "Spectral identification of topological domains, " Bioinf., vol. 32, no. 14, pp. 2151-2158, 2016. [Online]. Available: http://dx. doi. org/10. 1093/bioinformatics/ btw221
    • (2016) Bioinf. , vol.32 , Issue.14 , pp. 2151-2158
    • Chen, J.1    Hero, A.O.2    Rajapakse, I.3
  • 6
    • 84870305264 scopus 로고    scopus 로고
    • Wisdom of crowds for robust gene network inference
    • D. Marbach, et al., "Wisdom of crowds for robust gene network inference, " Nat. Meth., vol. 9, no. 8, pp. 796-804, 2012. [Online]. Available: http://www. nature. com/nmeth/journal/vaop/ ncurrent/full/nmeth. 2016. html
    • (2012) Nat. Meth. , vol.9 , Issue.8 , pp. 796-804
    • Marbach, D.1
  • 7
    • 84905028671 scopus 로고    scopus 로고
    • A comprehensive comparison of association estimators for gene network inference algorithms
    • Aug.
    • Z. Kurt, N. Aydin, and G. Altay, "A comprehensive comparison of association estimators for gene network inference algorithms, " Bioinf., vol. 30, no. 15, pp. 2142-2149, Aug. 2014. [Online]. Available: http://dx. doi. org/10. 1093/bioinformatics/btu182
    • (2014) Bioinf. , vol.30 , Issue.15 , pp. 2142-2149
    • Kurt, Z.1    Aydin, N.2    Altay, G.3
  • 8
    • 84926339771 scopus 로고    scopus 로고
    • Reverse engineering of genome-wide gene regulatory networks from gene expression data
    • Jan
    • Z.-P. Liu, "Reverse engineering of genome-wide gene regulatory networks from gene expression data, " Curr. Genom., vol. 16, no. 1, pp. 3-22, Jan 2015. [Online]. Available: http://dx. doi. org/ 10. 2174/1389202915666141110210634
    • (2015) Curr. Genom. , vol.16 , Issue.1 , pp. 3-22
    • Liu, Z.-P.1
  • 9
    • 0033655775 scopus 로고    scopus 로고
    • Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
    • Jan. 4-9
    • A. J. Butte and I. S. Kohane, "Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements, " in Pac. Symp. Biocomput., Jan. 4-9, 2000, pp. 415-429.
    • (2000) Pac. Symp. Biocomput. , pp. 415-429
    • Butte, A.J.1    Kohane, I.S.2
  • 10
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • J. J. Faith, et al., "Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles, " PLoS Biol., vol. 5, no. 1, pp. 54-66, 2007.
    • (2007) PLoS Biol. , vol.5 , Issue.1 , pp. 54-66
    • Faith, J.J.1
  • 11
    • 59949086432 scopus 로고    scopus 로고
    • Minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information
    • P. E. Meyer, F. Lafitte, and G. Bontempi, "minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information, " Bioinf., vol. 9, 2008, Art. no. 461.
    • (2008) Bioinf. , vol.9
    • Meyer, P.E.1    Lafitte, F.2    Bontempi, G.3
  • 12
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    • A. A. Margolin, et al., "ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context, " BMC Bioinf., vol. 7 no. Suppl. 1, no. 5, 2006, Art. no. S7.
    • (2006) BMC Bioinf. , vol.7 , Issue.5
    • Margolin, A.A.1
  • 13
    • 84871752758 scopus 로고    scopus 로고
    • NARROMI: A noise and redundancy reduction technique improves accuracy of gene regulatory network inference
    • X. Zhang, et al., "NARROMI: A noise and redundancy reduction technique improves accuracy of gene regulatory network inference, " Bioinf., vol. 29, no. 1, pp. 106-113, 2013. [Online]. Available: http://bioinformatics. oxfordjournals. org/content/29/ 1/106. abstract
    • (2013) Bioinf. , vol.29 , Issue.1 , pp. 106-113
    • Zhang, X.1
  • 14
    • 0036191190 scopus 로고    scopus 로고
    • Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling
    • Feb.
    • H. Toh and K. Horimoto, "Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling, " Bioinf., vol. 18, no. 2, pp. 287-297, Feb. 2002. [Online]. Available: http://dx. doi. org/10. 1093/bioinformatics/18. 2. 287
    • (2002) Bioinf. , vol.18 , Issue.2 , pp. 287-297
    • Toh, H.1    Horimoto, K.2
  • 15
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • Feb.
    • N. Friedman, "Inferring cellular networks using probabilistic graphical models, " Sci., vol. 303, no. 5659, pp. 799-805, Feb. 2004. [Online]. Available: http://dx. doi. org/10. 1126/science. 1094068
    • (2004) Sci. , vol.303 , Issue.5659 , pp. 799-805
    • Friedman, N.1
  • 16
    • 32644431906 scopus 로고    scopus 로고
    • Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks
    • Apr.
    • H. Lahdesmaki, S. Hautaniemi, I. Shmulevich, and O. Yli-Harja, "Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks, " Signal Process., vol. 86, no. 4, pp. 814-834, Apr. 2006. [Online]. Available: http://dx. doi. org/10. 1016/j. sigpro. 2005. 06. 008
    • (2006) Signal Process. , vol.86 , Issue.4 , pp. 814-834
    • Lahdesmaki, H.1    Hautaniemi, S.2    Shmulevich, I.3    Yli-Harja, O.4
  • 17
    • 38549107133 scopus 로고    scopus 로고
    • Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks
    • P. Li, C. Zhang, E. J. Perkins, P. Gong, and Y. Deng, "Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks, " BMC Bioinf., vol. 8, no. Suppl. 7, 2007, Art. no. S13. [Online]. Available: http:// dx. doi. org/10. 1186/1471-2105-8-S7-S13
    • (2007) BMC Bioinf. , vol.8
    • Li, P.1    Zhang, C.2    Perkins, E.J.3    Gong, P.4    Deng, Y.5
  • 18
    • 59549086094 scopus 로고    scopus 로고
    • SIMoNe: Statistical inference for MOdular NEtworks
    • J. Chiquet, A. Smith, G. Grasseau, C. Matias, and C. Ambroise, "SIMoNe: Statistical inference for MOdular NEtworks, " Bioinf., vol. 25, no. 3, pp. 417-418, 2009.
    • (2009) Bioinf. , vol.25 , Issue.3 , pp. 417-418
    • Chiquet, J.1    Smith, A.2    Grasseau, G.3    Matias, C.4    Ambroise, C.5
  • 19
    • 78650101617 scopus 로고    scopus 로고
    • Covariance estimation in decomposable Gaussian graphical models
    • Mar.
    • A. Wiesel, Y. C. Eldar, and A. O. Hero III, "Covariance estimation in decomposable Gaussian graphical models, " IEEE Trans. Signal Process., vol. 58, no. 3, pp. 1482-1492, Mar. 2010. [Online]. Available: http://dx. doi. org/10. 1109/TSP. 2009. 2037350
    • (2010) IEEE Trans. Signal Process. , vol.58 , Issue.3 , pp. 1482-1492
    • Wiesel, A.1    Eldar, Y.C.2    Hero, A.O.3
  • 20
    • 84910070867 scopus 로고    scopus 로고
    • Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza a virus infection
    • Z.-P. Liu, H. Wu, J. Zhu, and H. Miao, "Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza a virus infection, " BMC Bioinf., vol. 15, no. 1, 2014, Art. no. 336. [Online]. Available: http://dx. doi. org/10. 1186/1471-2105-15-336
    • (2014) BMC Bioinf. , vol.15 , Issue.1
    • Liu, Z.-P.1    Wu, H.2    Zhu, J.3    Miao, H.4
  • 21
    • 84943257078 scopus 로고    scopus 로고
    • RegNetwork: An integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse
    • Z.-P. Liu, C. Wu, H. Miao, and H. Wu, "RegNetwork: An integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse, " Database, vol. 2015, 2015. [Online]. Available: http://dx. doi. org/10. 1093/database/bav095
    • (2015) Database , vol.2015
    • Liu, Z.-P.1    Wu, C.2    Miao, H.3    Wu, H.4
  • 22
    • 77958570788 scopus 로고    scopus 로고
    • Inferring regulatory networks from expression data using treebased methods
    • Sep.
    • V. A. Huynh-Thu, A. Irrthum, L. Wehenkel, and P. Geurts, "Inferring regulatory networks from expression data using treebased methods, " PLoS One, vol. 5, no. 9, Sep. 2010, Art. no. e12776. [Online]. Available: http://dx. doi. org/10. 1371/ journal. pone. 0012776
    • (2010) PLoS One , vol.5 , Issue.9
    • Huynh-Thu, V.A.1    Irrthum, A.2    Wehenkel, L.3    Geurts, P.4
  • 23
    • 84946406582 scopus 로고    scopus 로고
    • BRANE Cut: Biologically-related a priori network enhancement with graph cuts for gene regulatory network inference
    • Dec.
    • A. Pirayre, C. Couprie, F. Bidard, L. Duval, and J.-C. Pesquet, "BRANE Cut: Biologically-related a priori network enhancement with graph cuts for gene regulatory network inference, " BMC Bioinf., vol. 16, no. 1, Dec. 2015, Art. no. 369. [Online]. Available: http://dx. doi. org/10. 1186/s12859-015-0754-2
    • (2015) BMC Bioinf. , vol.16 , Issue.1
    • Pirayre, A.1    Couprie, C.2    Bidard, F.3    Duval, L.4    Pesquet, J.-C.5
  • 24
    • 85011628753 scopus 로고    scopus 로고
    • Enhancing gene regulatory network inference through data integration with MarKov random fields
    • Feb.
    • M. Banf and S. Y. Rhee, "Enhancing gene regulatory network inference through data integration with MarKov random fields, " Sci. Rep., vol. 7, Feb. 2017, Art. no. 41174. [Online]. Available: http://dx. doi. org/10. 1038/srep41174
    • (2017) Sci. Rep. , vol.7
    • Banf, M.1    Rhee, S.Y.2
  • 25
    • 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 Bioinf., vol. 9, no. 1, 2008, Art. no. 559. [Online]. Available: http://dx. doi. org/ 10. 1186/1471-2105-9-559
    • (2008) BMC Bioinf. , vol.9 , Issue.1
    • Langfelder, P.1    Horvath, S.2
  • 26
    • 84255196314 scopus 로고    scopus 로고
    • Communities, modules and large-scale structure in networks
    • M. E. J. Newman, "Communities, modules and large-scale structure in networks, " Nat. Phys., vol. 8, no. 1, pp. 25-31, 2012. [Online]. Available: http://dx. doi. org/10. 1038/nphys2162
    • (2012) Nat. Phys. , vol.8 , Issue.1 , pp. 25-31
    • Newman, M.E.J.1
  • 27
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
    • May
    • E. Segal, et al., "Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data, " Nat. Genet., vol. 34, no. 2, pp. 166-176, May 2003. [Online]. Available: http://dx. doi. org/10. 1038/ng1165
    • (2003) Nat. Genet. , vol.34 , Issue.2 , pp. 166-176
    • Segal, E.1
  • 28
    • 60149110901 scopus 로고    scopus 로고
    • Module networks revisited: Computational assessment and prioritization of model predictions
    • 2009
    • A. Joshi, R. De Smet, K. Marchal, Y. Van de Peer, and T. Michoel, "Module networks revisited: Computational assessment and prioritization of model predictions. " Bioinf., vol. 25, no. 4, pp. 490-496, 2009. [Online]. Available: http://dx. doi. org/10. 1093/ bioinformatics/btn658
    • Bioinf. , vol.25 , Issue.4 , pp. 490-496
    • Joshi, A.1    De Smet, R.2    Marchal, K.3    Van de Peer, Y.4    Michoel, T.5
  • 29
    • 84887283985 scopus 로고    scopus 로고
    • Integrated module and gene-specific regulatory inference implicates upstream signaling networks
    • Oct.
    • S. Roy, S. Lagree, Z. Hou, J. A. Thomson, R. Stewart, and A. P. Gasch, "Integrated module and gene-specific regulatory inference implicates upstream signaling networks, " PLoS Comput. Biol., vol. 9, no. 10, Oct. 2013, Art. no. e1003252. [Online]. Available: http://dx. doi. org/10. 1371/journal. pcbi. 1003252
    • (2013) PLoS Comput. Biol. , vol.9 , Issue.10
    • Roy, S.1    Lagree, S.2    Hou, Z.3    Thomson, J.A.4    Stewart, R.5    Gasch, A.P.6
  • 30
    • 84963983894 scopus 로고    scopus 로고
    • Graph inference enhancement with clustering: Application to gene regulatory network reconstruction
    • Aug. 31-Sep. 4
    • A. Pirayre, C. Couprie, L. Duval, and J.-C. Pesquet, "Graph inference enhancement with clustering: Application to gene regulatory network reconstruction, " in Proc. Eur. Sig. Image Proc. Conf., Aug. 31-Sep. 4, 2015, pp. 2406-2410. [Online]. Available: http:// dx. doi. org/10. 1109/EUSIPCO. 2015. 7362816
    • (2015) Proc. Eur. Sig. Image Proc. Conf. , pp. 2406-2410
    • Pirayre, A.1    Couprie, C.2    Duval, L.3    Pesquet, J.-C.4
  • 31
    • 33846207510 scopus 로고    scopus 로고
    • Random walks for image segmentation
    • Nov.
    • L. Grady, "Random walks for image segmentation, " IEEE Trans. Pattern Anal. Mach. Intell., vol. 28, no. 11, pp. 1768-1783, Nov. 2006. [Online]. Available: http://dx. doi. org/10. 1109/ TPAMI. 2006. 233
    • (2006) IEEE Trans. Pattern Anal. Mach. Intell. , vol.28 , Issue.11 , pp. 1768-1783
    • Grady, L.1
  • 32
    • 59649110273 scopus 로고    scopus 로고
    • Generating realistic in silico gene networks for performance assessment of reverse engineering methods
    • Feb.
    • D. Marbach, T. Schaffter, C. Mattiussi, and D. Floreano, "Generating realistic in silico gene networks for performance assessment of reverse engineering methods, " J. Comput. Biol., vol. 16, no. 2, pp. 229-239, Feb. 2009. [Online]. Available: http:// dx. doi. org/10. 1089/cmb. 2008. 09TT
    • (2009) J. Comput. Biol. , vol.16 , Issue.2 , pp. 229-239
    • Marbach, D.1    Schaffter, T.2    Mattiussi, C.3    Floreano, D.4
  • 33
    • 79961200389 scopus 로고    scopus 로고
    • GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods
    • T. Schaffter, D. Marbach, and D. Floreano, "GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods, " Bioinf., vol. 27, no. 16, pp. 2263-2270, 2011. [Online]. Available: http://dx. doi. org/10. 1093/ bioinformatics/btr373
    • (2011) Bioinf. , vol.27 , Issue.16 , pp. 2263-2270
    • Schaffter, T.1    Marbach, D.2    Floreano, D.3
  • 34
    • 84876515907 scopus 로고    scopus 로고
    • STRING v9. 1: Protein-protein interaction networks, with increased coverage and integration
    • A. Franceschini, et al., "STRING v9. 1: Protein-protein interaction networks, with increased coverage and integration, " Nucleic Acids Res., vol. 41, pp. D808-D815, 2013.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D808-D815
    • Franceschini, A.1
  • 35
    • 13444249988 scopus 로고    scopus 로고
    • STRING: Known and predicted proteinprotein associations, integrated and transferred across organisms
    • Jan.
    • C. von Mering, et al., "STRING: Known and predicted proteinprotein associations, integrated and transferred across organisms, " Nucleic Acids Res., vol. 33, no. Suppl. 1, pp. D433-D437, Jan. 2005. [Online]. Available: http://dx. doi. org/10. 1093/nar/gki005
    • (2005) Nucleic Acids Res. , vol.33 , pp. D433-D437
    • Von Mering, C.1
  • 36
    • 0001820920 scopus 로고    scopus 로고
    • X-means: Extending K-means with efficient estimation of the number of clusters
    • Jun. 29-Jul. 2
    • D. Pelleg and A. Moore, "X-means: Extending K-means with efficient estimation of the number of clusters, " in Proc. Int. Conf. Mach. Learn., Jun. 29-Jul. 2, 2000, pp. 727-734.
    • (2000) Proc. Int. Conf. Mach. Learn. , pp. 727-734
    • Pelleg, D.1    Moore, A.2
  • 37
    • 33747479974 scopus 로고
    • Sur la division des corps mat-eriels en parties
    • H. Steinhaus, "Sur la division des corps mat-eriels en parties, " Bull. Acad. Polon. Sci., vol. Cl. III-vol. IV, no. 12, pp. 801-804, 1956.
    • (1956) Bull. Acad. Polon. Sci. Cl. III , vol.4 , Issue.12 , pp. 801-804
    • Steinhaus, H.1
  • 38
    • 0001457509 scopus 로고
    • Some methods for classification and analysis of multivariate observations
    • J. MacQueen, "Some methods for classification and analysis of multivariate observations, " in Proc. Fifth Berkeley Symp. Math. Statist. Prob., 1967, pp. 281-297.
    • (1967) Proc. Fifth Berkeley Symp. Math. Statist. Prob. , pp. 281-297
    • MacQueen, J.1
  • 39
    • 84860329104 scopus 로고    scopus 로고
    • Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars
    • Sep.
    • M. Wang, et al., "Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars, " Theor. Appl. Genet., vol. 124, no. 2, pp. 233-246, Sep. 2012. [Online]. Available: http://dx. doi. org/10. 1007/s00122-011-1697-2
    • (2012) Theor. Appl. Genet. , vol.124 , Issue.2 , pp. 233-246
    • Wang, M.1
  • 40
    • 84949981475 scopus 로고    scopus 로고
    • Transcriptomic characterization of an infection of Mycobacterium smegmatis by the cluster A4 mycobacteriophage Kampy
    • Oct.
    • A. Halleran, S. Clamons, and M. Saha, "Transcriptomic characterization of an infection of Mycobacterium smegmatis by the cluster A4 mycobacteriophage Kampy, " PLoS One, vol. 10, no. 10, Oct. 2015, Art. no. e0141100. [Online]. Available: http://dx. doi. org/10. 1371/journal. pone. 0141100
    • (2015) PLoS One , vol.10 , Issue.10
    • Halleran, A.1    Clamons, S.2    Saha, M.3
  • 41
    • 33947156744 scopus 로고    scopus 로고
    • Comparing clusterings-an information based distance
    • May
    • M. Meil-a, "Comparing clusterings-an information based distance, " J. Multivariate Anal., vol. 98, no. 5, pp. 873-895, May 2007. [Online]. Available: http://dx. doi. org/10. 1016/j. jmva. 2006. 11. 013
    • (2007) J. Multivariate Anal. , vol.98 , Issue.5 , pp. 873-895
    • Meila, M.1
  • 42
    • 84976874666 scopus 로고    scopus 로고
    • RegulonDB version 9. 0: High-level integration of gene regulation, coexpression, motif clustering and beyond
    • S. Gama-Castro, et al., "RegulonDB version 9. 0: High-level integration of gene regulation, coexpression, motif clustering and beyond, " Nucleic Acids Res., vol. 44, no. D1, pp. D133-D143, 2016. [Online]. Available: http://dx. doi. org/10. 1093/nar/gkv1156
    • (2016) Nucleic Acids Res. , vol.44 , Issue.D1 , pp. D133-D143
    • Gama-Castro, S.1


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