메뉴 건너뛰기




Volumn 5, Issue AUG, 2014, Pages

Untangling statistical and biological models to understand network inference: The need for a genomics network ontology

Author keywords

Computational genomics; Epistemology; Gene regulatory networks; Genomics network ontology; Mathematical modeling; Statistical inference; Systems biology

Indexed keywords

DNA; MESSENGER RNA; TRANSCRIPTION FACTOR;

EID: 84906234734     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00299     Document Type: Article
Times cited : (15)

References (39)
  • 1
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • Friedman, N. (2004) Inferring cellular networks using probabilistic graphical models. Science 303 799-805.
    • (2004) Science , vol.303 , pp. 799-805
    • Friedman, N.1
  • 2
    • 22044448669 scopus 로고    scopus 로고
    • Sparse graphical gaussian modeling of the isoprenoid gene network in arabidopsis thaliana
    • Wille, A., Zimmermann, P., Vranova, E., Furholz, A., Laule, O., Bleuler, S., et al. (2004) Sparse graphical gaussian modeling of the isoprenoid gene network in arabidopsis thaliana. Genome Biology 5 R92.
    • (2004) Genome Biology , vol.5
    • Wille, A.1    Zimmermann, P.2    Vranova, E.3    Furholz, A.4    Laule, O.5    Bleuler, S.6
  • 3
    • 84873169138 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from gene expression data by PC-algorithm based on conditional mutual information
    • Zhang, X., Zhao, X.-M., He, K., Lu, L., Cao, Y., Liu, J., et al. (2011) Inferring gene regulatory networks from gene expression data by PC-algorithm based on conditional mutual information. Bioinformatics.
    • (2011) ioinformatics
    • Zhang, X.1    Zhao, X.-M.2    He, K.3    Lu, L.4    Cao, Y.5    Liu, J.6
  • 4
    • 61349180117 scopus 로고    scopus 로고
    • Gene regulatory network inference: Data integration in dynamic models - A review
    • Hecker, M., Lambeck, S., Toepfer, S., van Someren, E., and Guthke, R. (2009) Gene regulatory network inference: Data integration in dynamic models - A review. Biosystems 96 86 - 103.
    • (2009) Biosystems , vol.96 , pp. 86-103
    • Hecker, M.1    Lambeck, S.2    Toepfer, S.3    van Someren, E.4    Guthke, R.5
  • 5
    • 33750016109 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from multiple microarray datasets
    • Wang, Y., Joshi, T., Zhang, X.-S., Xu, D., and Chen, L. (2006) Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics 22 2413-2420.
    • (2006) Bioinformatics , vol.22 , pp. 2413-2420
    • Wang, Y.1    Joshi, T.2    Zhang, X.-S.3    Xu, D.4    Chen, L.5
  • 6
    • 84987850256 scopus 로고    scopus 로고
    • Quantitative Assessment and Validation of Network Inference Methods in Bioinformatics
    • Haibe-Kains, B. and Emmert-Streib, F. (2014) Quantitative Assessment and Validation of Network Inference Methods in Bioinformatics. Front. Genet. 5 221.
    • (2014) Front. Genet , vol.5 , pp. 221
    • Haibe-Kains, B.1    Emmert-Streib, F.2
  • 7
    • 84877302557 scopus 로고    scopus 로고
    • Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information
    • de Matos Simoes, R., Dehmer, M., and Emmert-Streib, F. (2013) Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information. BMC Genomics 14 324.
    • (2013) BMC Genomics , vol.14 , pp. 324
    • de Matos Simoes, R.1    Dehmer, M.2    Emmert-Streib, F.3
  • 8
    • 84859112389 scopus 로고    scopus 로고
    • Statistical inference and reverse engineering of gene regulatory networks from observational expression data
    • Emmert-Streib, F., Glazko, G., Altay, G., and de Matos Simoes, R. (2012) Statistical inference and reverse engineering of gene regulatory networks from observational expression data. Frontiers in Genetics 3 8.
    • (2012) Frontiers in Genetics , vol.3 , pp. 8
    • Emmert-Streib, F.1    Glazko, G.2    Altay, G.3    de Matos Simoes, R.4
  • 9
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    • Margolin, A., Nemenman, I., Basso, K., Wiggins, C., and Stolovitzky et al, G. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7 S7.
    • (2006) BMC Bioinformatics , vol.7
    • Margolin, A.1    Nemenman, I.2    Basso, K.3    Wiggins, C.4    Stolovitzky, G.5
  • 10
    • 59949086432 scopus 로고    scopus 로고
    • minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information
    • Meyer, P., Lafitte, F., and Bontempi, G. (2008) minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information. BMC Bioinformatics 9 461.
    • (2008) BMC Bioinformatics , vol.9 , pp. 461
    • Meyer, P.1    Lafitte, F.2    Bontempi, G.3
  • 12
    • 33749825955 scopus 로고    scopus 로고
    • Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
    • Werhli, A., Grzegorczyk, M., and Husmeier, D. (2006) Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics 22 2523-31.
    • (2006) Bioinformatics , vol.22 , pp. 2523-2531
    • Werhli, A.1    Grzegorczyk, M.2    Husmeier, D.3
  • 13
    • 77957141016 scopus 로고    scopus 로고
    • Inferring the conservative causal core of gene regulatory networks
    • Altay, G. and Emmert-Streib, F. (2010) Inferring the conservative causal core of gene regulatory networks. BMC Systems Biology 4 132.
    • (2010) BMC Systems Biology , vol.4 , pp. 132
    • Altay, G.1    Emmert-Streib, F.2
  • 14
    • 84859125037 scopus 로고    scopus 로고
    • Bagging statistical network inference from large-scale gene expression data
    • de Matos Simoes, R. and Emmert-Streib, F. (2012) Bagging statistical network inference from large-scale gene expression data. PLoS ONE 7 e33624.
    • (2012) PLoS ONE , vol.7
    • de Matos Simoes, R.1    Emmert-Streib, F.2
  • 15
    • 84886916597 scopus 로고    scopus 로고
    • ENNET: inferring large gene regulatory networks from expression data using gradient boosting
    • Slawek, J. and Arodz, T. (2013) ENNET: inferring large gene regulatory networks from expression data using gradient boosting. BMC Systems Biology 7 106.
    • (2013) BMC Systems Biology , vol.7 , pp. 106
    • Slawek, J.1    Arodz, T.2
  • 16
    • 77958570788 scopus 로고    scopus 로고
    • Inferring regulatory networks from expression data using tree-based methods
    • Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., and Geurts, P. (2010) Inferring regulatory networks from expression data using tree-based methods. PLoS ONE 5 e12776.
    • (2010) PLoS ONE , vol.5
    • Huynh-Thu, V.A.1    Irrthum, A.2    Wehenkel, L.3    Geurts, P.4
  • 17
    • 84899876508 scopus 로고    scopus 로고
    • Nimefi: Gene regulatory network inference using multiple ensemble feature importance algorithms
    • Ruyssinck, J., Huynh-Thu, V. A., Geurts, P., Dhaene, T., Demeester, P., and Saeys, Y. (2014) Nimefi: Gene regulatory network inference using multiple ensemble feature importance algorithms. PloS one 9 e92709.
    • (2014) PloS one , vol.9
    • Ruyssinck, J.1    Huynh-Thu, V.A.2    Geurts, P.3    Dhaene, T.4    Demeester, P.5    Saeys, Y.6
  • 18
    • 35649001607 scopus 로고
    • A quantitative description of the membrane current and its application to conduction and excitation in nerve
    • Hodgkin, A. and Huxley, A. (1952) A quantitative description of the membrane current and its application to conduction and excitation in nerve. J. Physiol. 117 500-544.
    • (1952) J. Physiol , vol.117 , pp. 500-544
    • Hodgkin, A.1    Huxley, A.2
  • 19
    • 36949064203 scopus 로고
    • Cardiac action and pacemaker potentials based on the Hodgkin-Huxley equations
    • NOBLE, D. (1960) Cardiac action and pacemaker potentials based on the Hodgkin-Huxley equations. Nature 188 495-97.
    • (1960) Nature , vol.188 , pp. 495-497
    • Noble, D.1
  • 20
    • 0031582628 scopus 로고    scopus 로고
    • Closed form solution for time-dependent enzyme kinetics
    • Schnell, S. and Mendoza, C. (1997) Closed form solution for time-dependent enzyme kinetics. Journal of Theoretical Biology 187 207-212. doi:http://dx.doi.org/10.1006/jtbi.1997.0425.
    • (1997) Journal of Theoretical Biology , vol.187 , pp. 207-212
    • Schnell, S.1    Mendoza, C.2
  • 21
    • 14844286390 scopus 로고    scopus 로고
    • Reverse-engineering transcription control networks
    • Gardner, T. S. and Faith, J. J. (2005) Reverse-engineering transcription control networks. Physics of Life Reviews 2 65 - 88.
    • (2005) Physics of Life Reviews , vol.2 , pp. 65-88
    • Gardner, T.S.1    Faith, J.J.2
  • 22
    • 52649087274 scopus 로고    scopus 로고
    • Modelling and analysis of gene regulatory networks
    • Karlebach, G. and Shamir, R. (2008) Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 9 770-780.
    • (2008) Nat Rev Mol Cell Biol , vol.9 , pp. 770-780
    • Karlebach, G.1    Shamir, R.2
  • 23
    • 84889612803 scopus 로고    scopus 로고
    • A model of genetic networks with delayed stochastic dynamics
    • Emmert-Streib, F. and Dehmer, M., eds. (Wiley-VCH, 2008)
    • Ribeiro, A., A model of genetic networks with delayed stochastic dynamics. Analysis ofMicroarray Data: A Network-based Approach, Emmert-Streib, F. and Dehmer, M., eds. (Wiley-VCH, 2008). 169-204.
    • Analysis ofMicroarray Data: A Network-based Approach , pp. 169-204
    • Ribeiro, A.1
  • 24
    • 0003694798 scopus 로고    scopus 로고
    • Origins of Order: Self-Organization and Selection in Evolution
    • (Oxford University Press, 1993)
    • Kauffman, S., Origins of Order: Self-Organization and Selection in Evolution (Oxford University Press, 1993).
    • Kauffman, S.1
  • 25
    • 0036184629 scopus 로고    scopus 로고
    • Probabilistic boolean networks: a rule-based uncertainty model for gene regulatory networks
    • Shmulevich, I., Dougherty, E. R., Kim, S., and Zhang, W. (2002) Probabilistic boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18 261-274.
    • (2002) Bioinformatics , vol.18 , pp. 261-274
    • Shmulevich, I.1    Dougherty, E.R.2    Kim, S.3    Zhang, W.4
  • 27
    • 33845369407 scopus 로고    scopus 로고
    • A general modeling strategy for gene regulatory networks with stochastic dynamics
    • Ribeiro, A., Zhu, R., and Kauffman, S. (2006) A general modeling strategy for gene regulatory networks with stochastic dynamics. Journal of Computational Biology 13 1630-1639.
    • (2006) Journal of Computational Biology , vol.13 , pp. 1630-1639
    • Ribeiro, A.1    Zhu, R.2    Kauffman, S.3
  • 29
    • 33144486498 scopus 로고    scopus 로고
    • SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms
    • Van den Bulcke, T., Van Leemput, K., Naudts, B., van Remortel, P., Ma, H., Verschoren, A., et al. (2006) SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinformatics 7 43.
    • (2006) BMC Bioinformatics , vol.7 , pp. 43
    • Van den Bulcke, T.1    Van Leemput, K.2    Naudts, B.3    van Remortel, P.4    Ma, H.5    Verschoren, A.6
  • 30
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • Gillespie, D. (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics 22 403-434.
    • (1976) Journal of Computational Physics , vol.22 , pp. 403-434
    • Gillespie, D.1
  • 31
    • 0033736476 scopus 로고    scopus 로고
    • Genetic network inference: from co-expression clustering to reverse engineering
    • D'haeseleer, P., Liang, S., and Somogyi, R. (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16 707-726.
    • (2000) Bioinformatics , vol.16 , pp. 707-726
    • D'haeseleer, P.1    Liang, S.2    Somogyi, R.3
  • 32
    • 34548388925 scopus 로고    scopus 로고
    • Inference of gene networks from temporal gene expression profiles
    • Bansal, M. and di Bernardo, D. (2007) Inference of gene networks from temporal gene expression profiles. IETSystBiol. 1306-12.
    • (2007) IETSystBiol , pp. 1306-1312
    • Bansal, M.1    di Bernardo, D.2
  • 33
    • 84896370627 scopus 로고    scopus 로고
    • A review on the computational approaches for gene regulatory network construction
    • Chai, L. E., Loh, S. K., Low, S. T., Mohamad, M. S., Deris, S., and Zakaria, Z. (2014) A review on the computational approaches for gene regulatory network construction. Computers in Biology and Medicine 48 55 - 65. doi:http://dx.doi.org/10.1016/j.compbiomed.2014.02.011.
    • (2014) Computers in Biology and Medicine , vol.48 , pp. 55-65
    • Chai, L.E.1    Loh, S.K.2    Low, S.T.3    Mohamad, M.S.4    Deris, S.5    Zakaria, Z.6
  • 34
    • 0043130707 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from time-ordered gene expression data of bacillus subtilis using differential equations
    • Hoon, M. D., Imoto, S., and Miyano, S., Inferring gene regulatory networks from time-ordered gene expression data of bacillus subtilis using differential equations. Pac. Symp. Biocomput (2003), 17-28.
    • (2003) Pac. Symp. Biocomput , pp. 17-28
    • Hoon, M.D.1    Imoto, S.2    Miyano, S.3
  • 35
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • de Jong, H. (2002) Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology 9 67-103.
    • (2002) Journal of Computational Biology , vol.9 , pp. 67-103
    • de Jong, H.1
  • 36
    • 0842309206 scopus 로고    scopus 로고
    • Inferring gene networks from time series microarray data using dynamic bayesian networks
    • doi:10.1093/bib/4.3.228
    • Kim, S. Y., Imoto, S., and Miyano, S. (2003) Inferring gene networks from time series microarray data using dynamic bayesian networks. Briefings in Bioinformatics 4 228-235. doi:10.1093/bib/4.3.228.
    • (2003) Briefings in Bioinformatics , vol.4 , pp. 228-235
    • Kim, S.Y.1    Imoto, S.2    Miyano, S.3
  • 38
    • 45849113320 scopus 로고    scopus 로고
    • On the epistemological crisis in genomics
    • Dougherty, E. R. (2008) On the epistemological crisis in genomics. Current genomics 9 69-79.
    • (2008) Current genomics , vol.9 , pp. 69-79
    • Dougherty, E.R.1
  • 39
    • 65949120704 scopus 로고    scopus 로고
    • Translational science: epistemology and the investigative process
    • Dougherty, E. R. (2009) Translational science: epistemology and the investigative process. Current genomics 10 102-109.
    • (2009) Current genomics , vol.10 , pp. 102-109
    • Dougherty, E.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.