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Volumn 26, Issue 2, 2014, Pages 520-537

Machine learning-based differential network analysis: A study of stress-responsive transcriptomes in Arabidopsis

Author keywords

[No Author keywords available]

Indexed keywords

SODIUM CHLORIDE; TRANSCRIPTOME;

EID: 84897076534     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.113.121913     Document Type: Article
Times cited : (90)

References (85)
  • 1
    • 66349129975 scopus 로고    scopus 로고
    • Toward a gold standard for promoter prediction evaluation
    • Abeel, T., Van de Peer, Y., and Saeys, Y. (2009). Toward a gold standard for promoter prediction evaluation. Bioinformatics 25: i313-i320.
    • (2009) Bioinformatics , vol.25
    • Abeel, T.1    Van de Peer, Y.2    Saeys, Y.3
  • 2
    • 37849020261 scopus 로고    scopus 로고
    • Network inference, analysis, and modeling in systems biology
    • Albert, R. (2007). Network inference, analysis, and modeling in systems biology. Plant Cell 19: 3327-3338.
    • (2007) Plant Cell , vol.19 , pp. 3327-3338
    • Albert, R.1
  • 4
    • 0042768158 scopus 로고    scopus 로고
    • Genome-wide insertional mutagenesis of Arabidopsis thaliana
    • Alonso, J.M., et al. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653-657.
    • (2003) Science , vol.301 , pp. 653-657
    • Alonso, J.M.1
  • 5
    • 84875994305 scopus 로고    scopus 로고
    • Dissection of regulatory networks that are altered in disease via differential co-expression
    • Amar, D., Safer, H., and Shamir, R. (2013). Dissection of regulatory networks that are altered in disease via differential co-expression. PLOS Comput. Biol. 9: e1002955.
    • (2013) PLOS Comput. Biol. , vol.9
    • Amar, D.1    Safer, H.2    Shamir, R.3
  • 6
    • 50349090461 scopus 로고    scopus 로고
    • Convergent energy and stress signaling
    • Baena-González, E., and Sheen, J. (2008). Convergent energy and stress signaling. Trends Plant Sci. 13: 474-482.
    • (2008) Trends Plant Sci. , vol.13 , pp. 474-482
    • Baena-González, E.1    Sheen, J.2
  • 7
    • 78649703966 scopus 로고    scopus 로고
    • Rewiring of genetic networks in response to DNA damage
    • Bandyopadhyay, S., et al. (2010). Rewiring of genetic networks in response to DNA damage. Science 330: 1385-1389.
    • (2010) Science , vol.330 , pp. 1385-1389
    • Bandyopadhyay, S.1
  • 9
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabási, A.L., and Oltvai, Z.N. (2004). Network biology: Understanding the cell's functional organization. Nat. Rev. Genet. 5: 101-113.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 101-113
    • Barabási, A.L.1    Oltvai, Z.N.2
  • 10
    • 84870724279 scopus 로고    scopus 로고
    • Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks
    • Bassel, G.W., Gaudinier, A., Brady, S.M., Hennig, L., Rhee, S.Y., and De Smet, I. (2012). Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell 24: 3859-3875.
    • (2012) Plant Cell , vol.24 , pp. 3859-3875
    • Bassel, G.W.1    Gaudinier, A.2    Brady, S.M.3    Hennig, L.4    Rhee, S.Y.5    De Smet, I.6
  • 11
    • 80054969308 scopus 로고    scopus 로고
    • Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets
    • Bassel, G.W., Glaab, E., Marquez, J., Holdsworth, M.J., and Bacardit, J. (2011). Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets. Plant Cell 23: 3101-3116.
    • (2011) Plant Cell , vol.23 , pp. 3101-3116
    • Bassel, G.W.1    Glaab, E.2    Marquez, J.3    Holdsworth, M.J.4    Bacardit, J.5
  • 12
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57: 289-300.
    • (1995) J. R. Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 13
    • 35148833196 scopus 로고    scopus 로고
    • Some unique properties of eigenvector centrality
    • Bonacich, P. (2007). Some unique properties of eigenvector centrality. Soc. Networks 29: 555-564.
    • (2007) Soc. Networks , vol.29 , pp. 555-564
    • Bonacich, P.1
  • 14
    • 69249085408 scopus 로고    scopus 로고
    • Stability and aggregation of ranked gene lists
    • Boulesteix, A.L., and Slawski, M. (2009). Stability and aggregation of ranked gene lists. Brief. Bioinform. 10: 556-568.
    • (2009) Brief. Bioinform. , vol.10 , pp. 556-568
    • Boulesteix, A.L.1    Slawski, M.2
  • 15
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman, L. (2001). Random forests. Mach. Learn. 45: 5-32.
    • (2001) Mach. Learn. , vol.45 , pp. 5-32
    • Breiman, L.1
  • 16
    • 84949130891 scopus 로고    scopus 로고
    • Rewiring makes the difference
    • Califano, A. (2011). Rewiring makes the difference. Mol. Syst. Biol. 7: 463.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 463
    • Califano, A.1
  • 17
  • 18
    • 5044245707 scopus 로고    scopus 로고
    • Gene co-expression network topology provides a framework for molecular characterization of cellular state
    • Carter, S.L., Brechbühler, C.M., Griffin, M., and Bond, A.T. (2004). Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics 20: 2242-2250.
    • (2004) Bioinformatics , vol.20 , pp. 2242-2250
    • Carter, S.L.1    Brechbühler, C.M.2    Griffin, M.3    Bond, A.T.4
  • 19
    • 28944444652 scopus 로고    scopus 로고
    • Differential coexpression analysis using microarray data and its application to human cancer
    • Choi, J.K., Yu, U., Yoo, O.J., and Kim, S. (2005). Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21: 4348-4355.
    • (2005) Bioinformatics , vol.21 , pp. 4348-4355
    • Choi, J.K.1    Yu, U.2    Yoo, O.J.3    Kim, S.4
  • 20
    • 0037276175 scopus 로고    scopus 로고
    • Statistical tests for differential expression in cDNA microarray experiments
    • Cui, X., and Churchill, G.A. (2003). Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 4: 210.
    • (2003) Genome Biol. , vol.4 , pp. 210
    • Cui, X.1    Churchill, G.A.2
  • 21
    • 77953913791 scopus 로고    scopus 로고
    • From 'differential expression' to 'differential networking'-Identification of dysfunctional regulatory networks in diseases
    • de la Fuente, A. (2010). From 'differential expression' to 'differential networking'-Identification of dysfunctional regulatory networks in diseases. Trends Genet. 26: 326-333.
    • (2010) Trends Genet. , vol.26 , pp. 326-333
    • de la Fuente, A.1
  • 22
    • 77957110013 scopus 로고    scopus 로고
    • Advantages and limitations of current network inference methods
    • De Smet, R., and Marchal, K. (2010). Advantages and limitations of current network inference methods. Nat. Rev. Microbiol. 8: 717-729.
    • (2010) Nat. Rev. Microbiol. , vol.8 , pp. 717-729
    • De Smet, R.1    Marchal, K.2
  • 23
    • 30644464444 scopus 로고    scopus 로고
    • Gene selection and classification of microarray data using random forest
    • Díaz-Uriarte, R., and Alvarez de Andrés, S. (2006). Gene selection and classification of microarray data using random forest. BMC Bioinformatics 7: 3.
    • (2006) BMC Bioinformatics , vol.7 , pp. 3
    • Díaz-Uriarte, R.1    Alvarez de Andrés, S.2
  • 24
    • 34548550573 scopus 로고    scopus 로고
    • Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
    • Elo, L.L., Järvenpää, H., Oresic, M., Lahesmaa, R., and Aittokallio, T. (2007). Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics 23: 2096-2103.
    • (2007) Bioinformatics , vol.23 , pp. 2096-2103
    • Elo, L.L.1    Järvenpää, H.2    Oresic, M.3    Lahesmaa, R.4    Aittokallio, T.5
  • 25
    • 79954414422 scopus 로고    scopus 로고
    • Arabidopsis paves the way: Genomic and network analyses in crops
    • Ferrier, T., Matus, J.T., Jin, J., and Riechmann, J.L. (2011). Arabidopsis paves the way: Genomic and network analyses in crops. Curr. Opin. Biotechnol. 22: 260-270.
    • (2011) Curr. Opin. Biotechnol. , vol.22 , pp. 260-270
    • Ferrier, T.1    Matus, J.T.2    Jin, J.3    Riechmann, J.L.4
  • 26
    • 33750177351 scopus 로고
    • Centrality in social networks: Concept clarification
    • Freeman, L.C. (1978). Centrality in social networks: Concept clarification. Soc. Networks 1: 215-239.
    • (1978) Soc. Networks , vol.1 , pp. 215-239
    • Freeman, L.C.1
  • 27
    • 84883162998 scopus 로고    scopus 로고
    • Reverse engineering: A key component of systems biology to unravel global abiotic stress cross-talk
    • Friedel, S., Usadel, B., von Wirén, N., and Sreenivasulu, N. (2012). Reverse engineering: A key component of systems biology to unravel global abiotic stress cross-talk. Front. Plant Sci. 3: 294.
    • (2012) Front. Plant Sci. , vol.3 , pp. 294
    • Friedel, S.1    Usadel, B.2    von Wirén, N.3    Sreenivasulu, N.4
  • 28
    • 33745210764 scopus 로고    scopus 로고
    • Crosstalk between abiotic and biotic stress responses: A current view from the points of convergence in the stress signaling networks
    • Fujita, M., Fujita, Y., Noutoshi, Y., Takahashi, F., Narusaka, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006). Crosstalk between abiotic and biotic stress responses: A current view from the points of convergence in the stress signaling networks. Curr. Opin. Plant Biol. 9: 436-442.
    • (2006) Curr. Opin. Plant Biol. , vol.9 , pp. 436-442
    • Fujita, M.1    Fujita, Y.2    Noutoshi, Y.3    Takahashi, F.4    Narusaka, Y.5    Yamaguchi-Shinozaki, K.6    Shinozaki, K.7
  • 29
    • 34548442971 scopus 로고    scopus 로고
    • Weighted gene coexpression network analysis strategies applied to mouse weight
    • Fuller, T.F., Ghazalpour, A., Aten, J.E., Drake, T.A., Lusis, A.J., and Horvath, S. (2007). Weighted gene coexpression network analysis strategies applied to mouse weight. Mamm. Genome 18: 463-472.
    • (2007) Mamm. Genome , vol.18 , pp. 463-472
    • Fuller, T.F.1    Ghazalpour, A.2    Aten, J.E.3    Drake, T.A.4    Lusis, A.J.5    Horvath, S.6
  • 30
    • 77950544798 scopus 로고    scopus 로고
    • A statistical framework for differential network analysis from microarray data
    • Gill, R., Datta, S., and Datta, S. (2010). A statistical framework for differential network analysis from microarray data. BMC Bioinformatics 11: 95.
    • (2010) BMC Bioinformatics , vol.11 , pp. 95
    • Gill, R.1    Datta, S.2    Datta, S.3
  • 31
    • 47249163800 scopus 로고    scopus 로고
    • Functional meta-analysis of double connectivity in gene coexpression networks in mammals
    • Gustin, M.P., Paultre, C.Z., Randon, J., Bricca, G., and Cerutti, C. (2008). Functional meta-analysis of double connectivity in gene coexpression networks in mammals. Physiol. Genomics 34: 34-41.
    • (2008) Physiol. Genomics , vol.34 , pp. 34-41
    • Gustin, M.P.1    Paultre, C.Z.2    Randon, J.3    Bricca, G.4    Cerutti, C.5
  • 32
    • 0007265820 scopus 로고
    • Eccentricity and centrality in networks
    • Hage, P., and Harary, F. (1995). Eccentricity and centrality in networks. Soc. Networks 17: 57-63.
    • (1995) Soc. Networks , vol.17 , pp. 57-63
    • Hage, P.1    Harary, F.2
  • 33
    • 34547131280 scopus 로고    scopus 로고
    • A robust measure of correlation between two genes on a microarray
    • Hardin, J., Mitani, A., Hicks, L., and VanKoten, B. (2007). A robust measure of correlation between two genes on a microarray. BMC Bioinformatics 8: 220.
    • (2007) BMC Bioinformatics , vol.8 , pp. 220
    • Hardin, J.1    Mitani, A.2    Hicks, L.3    VanKoten, B.4
  • 34
    • 32344446535 scopus 로고    scopus 로고
    • AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development
    • He, X.J., Mu, R.L., Cao, W.H., Zhang, Z.G., Zhang, J.S., and Chen, S.Y. (2005). AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J. 44: 903-916.
    • (2005) Plant J. , vol.44 , pp. 903-916
    • He, X.J.1    Mu, R.L.2    Cao, W.H.3    Zhang, Z.G.4    Zhang, J.S.5    Chen, S.Y.6
  • 35
    • 50949084896 scopus 로고    scopus 로고
    • Geometric interpretation of gene coexpression network analysis
    • Horvath, S., and Dong, J. (2008). Geometric interpretation of gene coexpression network analysis. PLOS Comput. Biol. 4: e1000117.
    • (2008) PLOS Comput. Biol. , vol.4
    • Horvath, S.1    Dong, J.2
  • 36
    • 84864374040 scopus 로고    scopus 로고
    • Beyond differential expression: The quest for causal mutations and effector molecules
    • Hudson, N.J., Dalrymple, B.P., and Reverter, A. (2012). Beyond differential expression: The quest for causal mutations and effector molecules. BMC Genomics 13: 356.
    • (2012) BMC Genomics , vol.13 , pp. 356
    • Hudson, N.J.1    Dalrymple, B.P.2    Reverter, A.3
  • 37
    • 67049159812 scopus 로고    scopus 로고
    • A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation
    • Hudson, N.J., Reverter, A., and Dalrymple, B.P. (2009). A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLOS Comput. Biol. 5: e1000382.
    • (2009) PLOS Comput. Biol. , vol.5
    • Hudson, N.J.1    Reverter, A.2    Dalrymple, B.P.3
  • 38
    • 80052394788 scopus 로고    scopus 로고
    • Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network
    • Hwang, S., Rhee, S.Y., Marcotte, E.M., and Lee, I. (2011). Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nat. Protoc. 6: 1429-1442.
    • (2011) Nat. Protoc. , vol.6 , pp. 1429-1442
    • Hwang, S.1    Rhee, S.Y.2    Marcotte, E.M.3    Lee, I.4
  • 40
    • 84856094560 scopus 로고    scopus 로고
    • Differential network biology
    • Ideker, T., and Krogan, N.J. (2012). Differential network biology. Mol. Syst. Biol. 8: 565.
    • (2012) Mol. Syst. Biol. , vol.8 , pp. 565
    • Ideker, T.1    Krogan, N.J.2
  • 41
    • 0036840274 scopus 로고    scopus 로고
    • Salt-stressinduced ABA accumulation is more sensitively triggered in roots than in shoots
    • Jia, W., Wang, Y., Zhang, S., and Zhang, J. (2002). Salt-stressinduced ABA accumulation is more sensitively triggered in roots than in shoots. J. Exp. Bot. 53: 2201-2206.
    • (2002) J. Exp. Bot. , vol.53 , pp. 2201-2206
    • Jia, W.1    Wang, Y.2    Zhang, S.3    Zhang, J.4
  • 42
    • 34547596338 scopus 로고    scopus 로고
    • MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features
    • Jiang, P., Wu, H., Wang, W., Ma, W., Sun, X., and Lu, Z. (2007). MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 35: W339-W344.
    • (2007) Nucleic Acids Res. , vol.35
    • Jiang, P.1    Wu, H.2    Wang, W.3    Ma, W.4    Sun, X.5    Lu, Z.6
  • 43
    • 33750367871 scopus 로고    scopus 로고
    • Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes
    • Jiang, Y., and Deyholos, M.K. (2006). Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes. BMC Plant Biol. 6: 25.
    • (2006) BMC Plant Biol. , vol.6 , pp. 25
    • Jiang, Y.1    Deyholos, M.K.2
  • 45
    • 34247200577 scopus 로고    scopus 로고
    • The AtGenExpress global stress expression data set: Protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
    • Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E., Kudla, J., and Harter, K. (2007). The AtGenExpress global stress expression data set: Protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 50: 347-363.
    • (2007) Plant J. , vol.50 , pp. 347-363
    • Kilian, J.1    Whitehead, D.2    Horak, J.3    Wanke, D.4    Weinl, S.5    Batistic, O.6    D'Angelo, C.7    Bornberg-Bauer, E.8    Kudla, J.9    Harter, K.10
  • 46
    • 84880943554 scopus 로고    scopus 로고
    • Data integration through proximity-based networks provides biological principles of organization across scales
    • Kleessen, S., Klie, S., and Nikoloski, Z. (2013). Data integration through proximity-based networks provides biological principles of organization across scales. Plant Cell 25: 1917-1927.
    • (2013) Plant Cell , vol.25 , pp. 1917-1927
    • Kleessen, S.1    Klie, S.2    Nikoloski, Z.3
  • 47
    • 78650335757 scopus 로고    scopus 로고
    • Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate
    • Krouk, G., Mirowski, P., LeCun, Y., Shasha, D.E., and Coruzzi, G.M. (2010). Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biol. 11: R123.
    • (2010) Genome Biol. , vol.11
    • Krouk, G.1    Mirowski, P.2    LeCun, Y.3    Shasha, D.E.4    Coruzzi, G.M.5
  • 48
    • 80054106797 scopus 로고    scopus 로고
    • Role of DREBs in regulation of abiotic stress responses in plants
    • Lata, C., and Prasad, M. (2011). Role of DREBs in regulation of abiotic stress responses in plants. J. Exp. Bot. 62: 4731-4748.
    • (2011) J. Exp. Bot. , vol.62 , pp. 4731-4748
    • Lata, C.1    Prasad, M.2
  • 49
    • 76349125292 scopus 로고    scopus 로고
    • Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
    • Lee, I., Ambaru, B., Thakkar, P., Marcotte, E.M., and Rhee, S.Y. (2010). Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat. Biotechnol. 28: 149-156.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 149-156
    • Lee, I.1    Ambaru, B.2    Thakkar, P.3    Marcotte, E.M.4    Rhee, S.Y.5
  • 50
    • 79957754723 scopus 로고    scopus 로고
    • Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues
    • Less, H., Angelovici, R., Tzin, V., and Galili, G. (2011). Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues. Plant Cell 23: 1264-1271.
    • (2011) Plant Cell , vol.23 , pp. 1264-1271
    • Less, H.1    Angelovici, R.2    Tzin, V.3    Galili, G.4
  • 51
    • 80052776231 scopus 로고    scopus 로고
    • A dynamic programming algorithm for identification of triplex-forming sequences
    • Lexa, M., Martínek, T., Burgetová, I., Kopecek, D., and Brázdová, M. (2011). A dynamic programming algorithm for identification of triplex-forming sequences. Bioinformatics 27: 2510-2517.
    • (2011) Bioinformatics , vol.27 , pp. 2510-2517
    • Lexa, M.1    Martínek, T.2    Burgetová, I.3    Kopecek, D.4    Brázdová, M.5
  • 52
    • 84861706209 scopus 로고    scopus 로고
    • Gene-sharing networks reveal organizing principles of transcriptomes in Arabidopsis and other multicellular organisms
    • Li, S., Pandey, S., Gookin, T.E., Zhao, Z., Wilson, L., and Assmann, S.M. (2012). Gene-sharing networks reveal organizing principles of transcriptomes in Arabidopsis and other multicellular organisms. Plant Cell 24: 1362-1378.
    • (2012) Plant Cell , vol.24 , pp. 1362-1378
    • Li, S.1    Pandey, S.2    Gookin, T.E.3    Zhao, Z.4    Wilson, L.5    Assmann, S.M.6
  • 53
    • 77957813589 scopus 로고    scopus 로고
    • DCGL: An R package for identifying differentially coexpressed genes and links from gene expression microarray data
    • Liu, B.H., Yu, H., Tu, K., Li, C., Li, Y.X., and Li, Y.Y. (2010). DCGL: An R package for identifying differentially coexpressed genes and links from gene expression microarray data. Bioinformatics 26: 2637-2638.
    • (2010) Bioinformatics , vol.26 , pp. 2637-2638
    • Liu, B.H.1    Yu, H.2    Tu, K.3    Li, C.4    Li, Y.X.5    Li, Y.Y.6
  • 54
    • 55849151275 scopus 로고    scopus 로고
    • Systems approaches to identifying gene regulatory networks in plants
    • Long, T.A., Brady, S.M., and Benfey, P.N. (2008). Systems approaches to identifying gene regulatory networks in plants. Annu. Rev. Cell Dev. Biol. 24: 81-103.
    • (2008) Annu. Rev. Cell Dev. Biol. , vol.24 , pp. 81-103
    • Long, T.A.1    Brady, S.M.2    Benfey, P.N.3
  • 55
    • 84884518215 scopus 로고    scopus 로고
    • Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data
    • López-Kleine, L., Leal, L., and López, C. (2013). Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data. Brief Funct. Genomics 12: 457-467.
    • (2013) Brief Funct. Genomics , vol.12 , pp. 457-467
    • López-Kleine, L.1    Leal, L.2    López, C.3
  • 56
    • 84879137062 scopus 로고    scopus 로고
    • Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening
    • Luhua, S., et al. (2013). Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening. Physiol. Plant. 148: 322-333.
    • (2013) Physiol. Plant. , vol.148 , pp. 322-333
    • Luhua, S.1
  • 57
    • 84865842920 scopus 로고    scopus 로고
    • Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis
    • Ma, C., and Wang, X. (2012). Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis. Plant Physiol. 160: 192-203.
    • (2012) Plant Physiol. , vol.160 , pp. 192-203
    • Ma, C.1    Wang, X.2
  • 58
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    • Maere, S., Heymans, K., and Kuiper, M. (2005). BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: 3448-3449.
    • (2005) Bioinformatics , vol.21 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 59
    • 28444441250 scopus 로고    scopus 로고
    • Cold, salinity and drought stresses: An overview
    • Mahajan, S., and Tuteja, N. (2005). Cold, salinity and drought stresses: An overview. Arch. Biochem. Biophys. 444: 139-158.
    • (2005) Arch. Biochem. Biophys. , vol.444 , pp. 139-158
    • Mahajan, S.1    Tuteja, N.2
  • 60
    • 84870305264 scopus 로고    scopus 로고
    • Wisdom of crowds for robust gene network inference
    • DREAM5 Consortium
    • Marbach, D., et al; DREAM5 Consortium (2012). Wisdom of crowds for robust gene network inference. Nat. Methods 9: 796-804.
    • (2012) Nat. Methods , vol.9 , pp. 796-804
    • Marbach, D.1
  • 61
    • 78649775562 scopus 로고    scopus 로고
    • Enrichment map: A network-based method for gene-set enrichment visualization and interpretation
    • Merico, D., Isserlin, R., Stueker, O., Emili, A., and Bader, G.D. (2010). Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS ONE 5: e13984.
    • (2010) PLoS ONE , vol.5
    • Merico, D.1    Isserlin, R.2    Stueker, O.3    Emili, A.4    Bader, G.D.5
  • 62
    • 0035860537 scopus 로고    scopus 로고
    • Machine learning for science: State of the art and future prospects
    • Mjolsness, E., and DeCoste, D. (2001). Machine learning for science: State of the art and future prospects. Science 293: 2051-2055.
    • (2001) Science , vol.293 , pp. 2051-2055
    • Mjolsness, E.1    DeCoste, D.2
  • 63
    • 77951168442 scopus 로고    scopus 로고
    • Omics meet networks-Using systems approaches to infer regulatory networks in plants
    • Moreno-Risueno, M.A., Busch, W., and Benfey, P.N. (2010). Omics meet networks-Using systems approaches to infer regulatory networks in plants. Curr. Opin. Plant Biol. 13: 126-131.
    • (2010) Curr. Opin. Plant Biol. , vol.13 , pp. 126-131
    • Moreno-Risueno, M.A.1    Busch, W.2    Benfey, P.N.3
  • 65
    • 84870790399 scopus 로고    scopus 로고
    • An ensemble correlation-based gene selection algorithm for cancer classification with gene expression data
    • Piao, Y., Piao, M., Park, K., and Ryu, K.H. (2012). An ensemble correlation-based gene selection algorithm for cancer classification with gene expression data. Bioinformatics 28: 3306-3315.
    • (2012) Bioinformatics , vol.28 , pp. 3306-3315
    • Piao, Y.1    Piao, M.2    Park, K.3    Ryu, K.H.4
  • 66
    • 44449145580 scopus 로고    scopus 로고
    • A comparative study of different machine learning methods on microarray gene expression data
    • Pirooznia, M., Yang, J.Y., Yang, M.Q., and Deng, Y. (2008). A comparative study of different machine learning methods on microarray gene expression data. BMC Genomics 9 (suppl. 1): S13.
    • (2008) BMC Genomics , vol.9 , Issue.SUPPL. 1
    • Pirooznia, M.1    Yang, J.Y.2    Yang, M.Q.3    Deng, Y.4
  • 70
    • 33745477457 scopus 로고    scopus 로고
    • Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression
    • Sakuma, Y., Maruyama, K., Osakabe, Y., Qin, F., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006). Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell 18: 1292-1309.
    • (2006) Plant Cell , vol.18 , pp. 1292-1309
    • Sakuma, Y.1    Maruyama, K.2    Osakabe, Y.3    Qin, F.4    Seki, M.5    Shinozaki, K.6    Yamaguchi-Shinozaki, K.7
  • 71
    • 0033421491 scopus 로고    scopus 로고
    • On the proper bounds of the Gini correlation
    • Schechtman, E., and Yitzhaki, S. (1999). On the proper bounds of the Gini correlation. Econ. Lett. 63: 6.
    • (1999) Econ. Lett. , vol.63 , pp. 6
    • Schechtman, E.1    Yitzhaki, S.2
  • 72
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth, G.K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3: e3.
    • (2004) Stat. Appl. Genet. Mol. Biol. , vol.3
    • Smyth, G.K.1
  • 73
    • 74249118093 scopus 로고    scopus 로고
    • Aging mice show a decreasing correlation of gene expression within genetic modules
    • Southworth, L.K., Owen, A.B., and Kim, S.K. (2009). Aging mice show a decreasing correlation of gene expression within genetic modules. PLoS Genet. 5: e1000776.
    • (2009) PLoS Genet. , vol.5
    • Southworth, L.K.1    Owen, A.B.2    Kim, S.K.3
  • 74
    • 30144433499 scopus 로고    scopus 로고
    • Enhanced tolerance to environmental stress in transgenic plants expressing the transcriptional coactivator multiprotein bridging factor 1c
    • Suzuki, N., Rizhsky, L., Liang, H., Shuman, J., Shulaev, V., and Mittler, R. (2005). Enhanced tolerance to environmental stress in transgenic plants expressing the transcriptional coactivator multiprotein bridging factor 1c. Plant Physiol. 139: 1313-1322.
    • (2005) Plant Physiol. , vol.139 , pp. 1313-1322
    • Suzuki, N.1    Rizhsky, L.2    Liang, H.3    Shuman, J.4    Shulaev, V.5    Mittler, R.6
  • 75
    • 84871787691 scopus 로고    scopus 로고
    • Data mining in the Life Sciences with Random Forest: A walk in the park or lost in the jungle? Brief
    • Touw, W.G., Bayjanov, J.R., Overmars, L., Backus, L., Boekhorst, J., Wels, M., and van Hijum, S.A. (2013). Data mining in the Life Sciences with Random Forest: A walk in the park or lost in the jungle? Brief. Bioinform. 14: 315-326.
    • (2013) Bioinform. , vol.14 , pp. 315-326
    • Touw, W.G.1    Bayjanov, J.R.2    Overmars, L.3    Backus, L.4    Boekhorst, J.5    Wels, M.6    van Hijum, S.A.7
  • 76
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98: 5116-5121.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 77
    • 77951687828 scopus 로고    scopus 로고
    • 'Omics' analyses of regulatory networks in plant abiotic stress responses
    • Urano, K., Kurihara, Y., Seki, M., and Shinozaki, K. (2010). 'Omics' analyses of regulatory networks in plant abiotic stress responses. Curr. Opin. Plant Biol. 13: 132-138.
    • (2010) Curr. Opin. Plant Biol. , vol.13 , pp. 132-138
    • Urano, K.1    Kurihara, Y.2    Seki, M.3    Shinozaki, K.4
  • 79
    • 84876760070 scopus 로고    scopus 로고
    • The potential of text mining in data integration and network biology for plant research: A case study on Arabidopsis
    • Van Landeghem, S., De Bodt, S., Drebert, Z.J., Inzé, D., and Van de Peer, Y. (2013). The potential of text mining in data integration and network biology for plant research: A case study on Arabidopsis. Plant Cell 25: 794-807.
    • (2013) Plant Cell , vol.25 , pp. 794-807
    • Van Landeghem, S.1    De Bodt, S.2    Drebert, Z.J.3    Inzé, D.4    Van de Peer, Y.5
  • 80
    • 33750416896 scopus 로고    scopus 로고
    • PSoL: A positive sample only learning algorithm for finding non-coding RNA genes
    • Wang, C., Ding, C., Meraz, R.F., and Holbrook, S.R. (2006). PSoL: A positive sample only learning algorithm for finding non-coding RNA genes. Bioinformatics 22: 2590-2596.
    • (2006) Bioinformatics , vol.22 , pp. 2590-2596
    • Wang, C.1    Ding, C.2    Meraz, R.F.3    Holbrook, S.R.4
  • 81
    • 84868288164 scopus 로고    scopus 로고
    • Arabidopsis defense against Botrytis cinerea: Chronology and regulation deciphered by high-resolution temporal transcriptomic analysis
    • Windram, O., et al. (2012). Arabidopsis defense against Botrytis cinerea: Chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. Plant Cell 24: 3530-3557.
    • (2012) Plant Cell , vol.24 , pp. 3530-3557
    • Windram, O.1
  • 82
    • 80655128625 scopus 로고    scopus 로고
    • Average rank-based score to measure deregulation of molecular pathway gene sets
    • Yang, H., Cheng, C., and Zhang, W. (2011). Average rank-based score to measure deregulation of molecular pathway gene sets. PLoS ONE 6: e27579.
    • (2011) PLoS ONE , vol.6
    • Yang, H.1    Cheng, C.2    Zhang, W.3
  • 83
    • 33744725160 scopus 로고    scopus 로고
    • Gini's mean difference: A superior measure of variability for non-normal distributions
    • Yitzhaki, S. (2003). Gini's mean difference: A superior measure of variability for non-normal distributions. METRON LXI: 285-316.
    • (2003) METRON , vol.61 , pp. 285-316
    • Yitzhaki, S.1
  • 84
    • 79960892858 scopus 로고    scopus 로고
    • Linkbased quantitative methods to identify differentially coexpressed genes and gene pairs
    • Yu, H., Liu, B.H., Ye, Z.Q., Li, C., Li, Y.X., and Li, Y.Y. (2011). Linkbased quantitative methods to identify differentially coexpressed genes and gene pairs. BMC Bioinformatics 12: 315.
    • (2011) BMC Bioinformatics , vol.12 , pp. 315
    • Yu, H.1    Liu, B.H.2    Ye, Z.Q.3    Li, C.4    Li, Y.X.5    Li, Y.Y.6
  • 85
    • 0036999615 scopus 로고    scopus 로고
    • Salt and drought stress signal transduction in plants
    • Zhu, J.K. (2002). Salt and drought stress signal transduction in plants. Annu. Rev. Plant Biol. 53: 247-273.
    • (2002) Annu. Rev. Plant Biol. , vol.53 , pp. 247-273
    • Zhu, J.K.1


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