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Volumn 9, Issue 2, 2014, Pages

Inferring nonlinear gene regulatory networks from gene expression data based on distance correlation

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLR DC; COMPARATIVE STUDY; DISTANCE CORRELATION; DNA REPAIR; ESCHERICHIA COLI; GENE EXPRESSION; GENE REGULATORY NETWORK; GENETIC DATABASE; INTERMETHOD COMPARISON; LEARNING ALGORITHM; MRNET DC; MUTUAL INFORMATION; NONHUMAN; NONLINEAR SYSTEM; PRECISION RECALL CURVE; RECEIVER OPERATING CHARACTERISTIC; REL DC; STATISTICAL ANALYSIS; STATISTICAL CONCEPTS;

EID: 84895822748     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0087446     Document Type: Article
Times cited : (49)

References (28)
  • 1
    • 0034616930 scopus 로고    scopus 로고
    • Functional discovery via a compendium of expression profiles
    • Hughes T, Marton M, Jones A, Roberts C, Stoughton R, et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
    • (2000) Cell , vol.102 , pp. 109-126
    • Hughes, T.1    Marton, M.2    Jones, A.3    Roberts, C.4    Stoughton, R.5
  • 4
    • 59649110273 scopus 로고    scopus 로고
    • Generating realistic in silico gene networks for performance assessment of reverse engineering methods
    • Marbach D, Schaffter T, Mattiussi C, Floreano D (2009) Generating realistic in silico gene networks for performance assessment of reverse engineering methods. Journal of Computational Biology 16: 229-239.
    • (2009) Journal of Computational Biology , vol.16 , pp. 229-239
    • Marbach, D.1    Schaffter, T.2    Mattiussi, C.3    Floreano, D.4
  • 7
    • 77955033717 scopus 로고    scopus 로고
    • Miss: A non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis
    • Brunel H, Gallardo-Chacón J, Buil A, Vallverdú M, Soria J, et al. (2010) Miss: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis. Bioinformatics 26: 1811-1818.
    • (2010) Bioinformatics , vol.26 , pp. 1811-1818
    • Brunel, H.1    Gallardo-Chacón, J.2    Buil, A.3    Vallverdú, M.4    Soria, J.5
  • 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, Stolovitzky G, et al. (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
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles
    • Faith J, Hayete B, Thaden J, Mogno I, Wierzbowski J, et al. (2007) Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS biology 5: e8.
    • (2007) PLoS Biology , vol.5
    • Faith, J.1    Hayete, B.2    Thaden, J.3    Mogno, I.4    Wierzbowski, J.5
  • 11
    • 0033655775 scopus 로고    scopus 로고
    • Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
    • Butte A, Kohane I (2000) Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. In: Pac Symp Biocomput. volume 5, 418-429.
    • (2000) Pac Symp Biocomput , vol.5 , pp. 418-429
    • Butte, A.1    Kohane, I.2
  • 12
    • 59949086432 scopus 로고    scopus 로고
    • minet: Ar/bioconductor package for inferring large transcriptional networks using mutual information
    • Meyer P, Lafitte F, Bontempi G (2008) minet: Ar/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
  • 13
    • 84855160951 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information
    • Zhang X, Zhao X, He K, Lu L, Cao Y, et al. (2012) Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinformatics 28: 98-104.
    • (2012) Bioinformatics , vol.28 , pp. 98-104
    • Zhang, X.1    Zhao, X.2    He, K.3    Lu, L.4    Cao, Y.5
  • 14
    • 84859125037 scopus 로고    scopus 로고
    • Bagging statistical network inference from large-scale gene expression data
    • de Matos Simoes R, 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
    • 0041877169 scopus 로고    scopus 로고
    • Estimation of entropy and mutual information
    • Paninski L (2003) Estimation of entropy and mutual information. Neural Computation 15: 1191-1253.
    • (2003) Neural Computation , vol.15 , pp. 1191-1253
    • Paninski, L.1
  • 16
    • 27844521293 scopus 로고    scopus 로고
    • A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics
    • Schäfer J, Strimmer K (2005) A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statistical applications in genetics and molecular biology 4: 32.
    • (2005) Statistical Applications in Genetics and Molecular Biology , vol.4 , pp. 32
    • Schäfer, J.1    Strimmer, K.2
  • 18
    • 77954479475 scopus 로고    scopus 로고
    • Local network-based measures to assess the inferability of different regulatory networks
    • Emmert-Streib F, Altay G (2010) Local network-based measures to assess the inferability of different regulatory networks. Systems Biology, IET 4: 277-288.
    • (2010) Systems Biology, IET , vol.4 , pp. 277-288
    • Emmert-Streib, F.1    Altay, G.2
  • 19
    • 50849124115 scopus 로고    scopus 로고
    • Measuring and testing dependence by correlation of distances
    • Székely G, Rizzo M, Bakirov N (2007) Measuring and testing dependence by correlation of distances. The Annals of Statistics 35: 2769-2794.
    • (2007) The Annals of Statistics , vol.35 , pp. 2769-2794
    • Székely, G.1    Rizzo, M.2    Bakirov, N.3
  • 24
    • 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, 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
  • 25
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of escherichia coli
    • Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of escherichia coli. Nature genetics 31: 64-68.
    • (2002) Nature Genetics , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 26
    • 58149349958 scopus 로고    scopus 로고
    • Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information
    • Luo W, Hankenson KD, Woolf PJ (2008) Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. BMC bioinformatics 9: 467.
    • (2008) BMC Bioinformatics , vol.9 , pp. 467
    • Luo, W.1    Hankenson, K.D.2    Woolf, P.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.