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Volumn 2013, Issue , 2013, Pages

Gene regulation, modulation, and their applications in gene expression data analysis

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EID: 84876588507     PISSN: 16878027     EISSN: 16878035     Source Type: Journal    
DOI: 10.1155/2013/360678     Document Type: Article
Times cited : (25)

References (54)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • 2-s2.0-0028806048
    • Schena M., Shalon D., Davis R. W., Brown P. O., Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995 270 5235 467 470 2-s2.0-0028806048
    • (1995) Science , vol.270 , Issue.5235 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 2
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • 2-s2.0-52949096084 10.1146/annurev.genom.9.081307.164359
    • Mardis E. R., Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics 2008 9 387 402 2-s2.0-52949096084 10.1146/annurev.genom.9.081307.164359
    • (2008) Annual Review of Genomics and Human Genetics , vol.9 , pp. 387-402
    • Mardis, E.R.1
  • 3
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Cancer Genome Atlas Network
    • Cancer Genome Atlas Network, Comprehensive molecular portraits of human breast tumours. Nature 2012 490 61 70
    • (2012) Nature , vol.490 , pp. 61-70
  • 9
    • 45149101194 scopus 로고    scopus 로고
    • Current approaches to gene regulatory network modelling
    • DOI 10.1186/1471-2105-8-S6-S9
    • Schlitt T., Brazma A., Current approaches to gene regulatory network modelling. BMC Bioinformatics 2007 8 supplement 6, article S9 2-s2.0-45149101194 10.1186/1471-2105-8-S6-S9 (Pubitemid 351833845)
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 6
    • Schlitt, T.1    Brazma, A.2
  • 10
    • 68349161006 scopus 로고    scopus 로고
    • Reverse engineering of gene regulatory networks: A comparative study
    • 2-s2.0-68149164746 10.1155/2009/617281 617281
    • Hache H., Lehrach H., Herwig R., Reverse engineering of gene regulatory networks: a comparative study. Eurasip Journal on Bioinformatics and Systems Biology 2009 2009 2-s2.0-68149164746 10.1155/2009/617281 617281
    • (2009) Eurasip Journal on Bioinformatics and Systems Biology , vol.2009
    • Hache, H.1    Lehrach, H.2    Herwig, R.3
  • 11
    • 67449095889 scopus 로고    scopus 로고
    • Computational methods for discovering gene networks from expression data
    • 2-s2.0-67449095889 10.1093/bib/bbp028
    • Lee W. P., Tzou W. S., Computational methods for discovering gene networks from expression data. Briefings in Bioinformatics 2009 10 4 408 423 2-s2.0-67449095889 10.1093/bib/bbp028
    • (2009) Briefings in Bioinformatics , vol.10 , Issue.4 , pp. 408-423
    • Lee, W.P.1    Tzou, W.S.2
  • 12
    • 70549083891 scopus 로고    scopus 로고
    • Inference of gene regulatory networks using time-series data: A survey
    • 2-s2.0-70549083891 10.2174/138920209789177610
    • Sima C., Hua J., Jung S., Inference of gene regulatory networks using time-series data: a survey. Current Genomics 2009 10 6 416 429 2-s2.0-70549083891 10.2174/138920209789177610
    • (2009) Current Genomics , vol.10 , Issue.6 , pp. 416-429
    • Sima, C.1    Hua, J.2    Jung, S.3
  • 13
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • DOI 10.1126/science.1087447
    • Stuart J. M., Segal E., Koller D., Kim S. K., A gene-coexpression network for global discovery of conserved genetic modules. Science 2003 302 5643 249 255 2-s2.0-0141993704 10.1126/science.1087447 (Pubitemid 37248749)
    • (2003) Science , vol.302 , Issue.5643 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 14
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    • DOI 10.1186/1471-2105-7-S1-S7
    • Margolin A. A., Nemenman I., Basso K., Wiggins C., Stolovitzky G., Favera R. D., Califano A., ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006 7 supplement 1, article S7 2-s2.0-33947305781 10.1186/1471-2105-7-S1-S7 (Pubitemid 46437495)
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL.1
    • Margolin, A.A.1    Nemenman, I.2    Basso, K.3    Wiggins, C.4    Stolovitzky, G.5    Favera, R.D.6    Califano, A.7
  • 15
    • 0034302007 scopus 로고    scopus 로고
    • Coefficient of determination in nonlinear signal processing
    • 2-s2.0-0034302007 10.1016/S0165-1684(00)00079-7
    • Dougherty E. R., Kim S., Chen Y., Coefficient of determination in nonlinear signal processing. Signal Processing 2000 80 10 2219 2235 2-s2.0-0034302007 10.1016/S0165-1684(00)00079-7
    • (2000) Signal Processing , vol.80 , Issue.10 , pp. 2219-2235
    • Dougherty, E.R.1    Kim, S.2    Chen, Y.3
  • 16
    • 0034661192 scopus 로고    scopus 로고
    • Multivariate measurement of gene expression relationships
    • DOI 10.1006/geno.2000.6241
    • Kim S., Dougherty E. R., Chen Y., Sivakumar K., Meltzer P., Trent J. M., Bittner M., Multivariate measurement of gene expression relationships. Genomics 2000 67 2 201 209 10.1006/geno.2000.6241 (Pubitemid 30614588)
    • (2000) Genomics , vol.67 , Issue.2 , pp. 201-209
    • Kim, S.1    Dougherty, E.R.2    Chen, Y.3    Sivakumar, K.4    Meltzer, P.5    Trent, J.M.6    Bittner, M.7
  • 17
    • 33751356890 scopus 로고    scopus 로고
    • BNArray: An R package for constructing gene regulatory networks from microarray data by using Bayesian network
    • DOI 10.1093/bioinformatics/btl491
    • Chen X., Chen M., Ning K., BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network. Bioinformatics 2006 22 23 2952 2954 2-s2.0-33751356890 10.1093/bioinformatics/ btl491 (Pubitemid 44811571)
    • (2006) Bioinformatics , vol.22 , Issue.23 , pp. 2952-2954
    • Chen, X.1    Chen, M.2    Ning, K.3
  • 18
    • 33749825955 scopus 로고    scopus 로고
    • Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
    • DOI 10.1093/bioinformatics/btl391
    • Werhli A. V., Grzegorczyk M., Husmeier D., Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics 2006 22 20 2523 2531 2-s2.0-33749825955 10.1093/bioinformatics/btl391 (Pubitemid 44560759)
    • (2006) Bioinformatics , vol.22 , Issue.20 , pp. 2523-2531
    • Werhli, A.V.1    Grzegorczyk, M.2    Husmeier, D.3
  • 19
    • 0036184629 scopus 로고    scopus 로고
    • Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks
    • Shmulevich I., Dougherty E. R., Kim S., Zhang W., Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 2002 18 2 261 274 2-s2.0-0036184629 (Pubitemid 34183104)
    • (2002) Bioinformatics , vol.18 , Issue.2 , pp. 261-274
    • Shmulevich, I.1    Dougherty, E.R.2    Kim, S.3    Zhang, W.4
  • 20
    • 80054689794 scopus 로고    scopus 로고
    • An extensive MicroRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma
    • 10.1016/j.cell.2011.09.041
    • Sumazin P., Yang X., Chiu H.-S., Chung W.-J., Llobet-Navas D., Rajbhandari P., Bansal M., Guarnieri P., Silva J., Califano A., An extensive MicroRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 2011 147 2 370 381 10.1016/j.cell.2011. 09.041
    • (2011) Cell , vol.147 , Issue.2 , pp. 370-381
    • Sumazin, P.1    Yang, X.2    Chiu, H.-S.3    Chung, W.-J.4    Llobet-Navas, D.5    Rajbhandari, P.6    Bansal, M.7    Guarnieri, P.8    Silva, J.9    Califano, A.10
  • 22
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • 2-s2.0-58249088751 10.1016/j.cell.2009.01.002
    • Bartel D. P., MicroRNAs: target recognition and regulatory functions. Cell 2009 136 2 215 233 2-s2.0-58249088751 10.1016/j.cell.2009.01.002
    • (2009) Cell , vol.136 , Issue.2 , pp. 215-233
    • Bartel, D.P.1
  • 23
    • 85032751589 scopus 로고    scopus 로고
    • Understanding MicroRNA regulation: A computational perspective
    • 6105465 10.1109/MSP.2011.943013
    • Yue D., Meng J., Lu M., Chen C. L. P., Guo M., Huang Y., Understanding MicroRNA regulation: a computational perspective. IEEE Signal Processing Magazine 2012 29 1 77 88 6105465 10.1109/MSP.2011.943013
    • (2012) IEEE Signal Processing Magazine , vol.29 , Issue.1 , pp. 77-88
    • Yue, D.1    Meng, J.2    Lu, M.3    Chen, C.L.P.4    Guo, M.5    Huang, Y.6
  • 24
    • 2942672580 scopus 로고    scopus 로고
    • Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA
    • DOI 10.1016/j.molcel.2004.05.027, PII S1097276504003284
    • Jones-Rhoades M. W., Bartel D. P., Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA. Molecular Cell 2004 14 6 787 799 2-s2.0-2942672580 10.1016/j.molcel.2004.05.027 (Pubitemid 38780852)
    • (2004) Molecular Cell , vol.14 , Issue.6 , pp. 787-799
    • Jones-Rhoades, M.W.1    Bartel, D.P.2
  • 25
    • 0034614637 scopus 로고    scopus 로고
    • The hallmarks of cancer
    • Hanahan D., Weinberg R. A., The hallmarks of cancer. Cell 2000 100 1 57 70 2-s2.0-0034614637 (Pubitemid 30046295)
    • (2000) Cell , vol.100 , Issue.1 , pp. 57-70
    • Hanahan, D.1    Weinberg, R.A.2
  • 26
    • 78149341677 scopus 로고    scopus 로고
    • Oncogenic KRAS modulates mitochondrial metabolism in human colon cancer cells by inducing HIF-1 α and HIF-2 α target genes
    • 2-s2.0-78149341677 10.1186/1476-4598-9-293
    • Chun S. Y., Johnson C., Washburn J. G., Cruz-Correa M. R., Dang D. T., Dang L. H., Oncogenic KRAS modulates mitochondrial metabolism in human colon cancer cells by inducing HIF-1 α and HIF-2 α target genes. Molecular Cancer 2010 9, article 293 2-s2.0-78149341677 10.1186/1476-4598-9-293
    • (2010) Molecular Cancer , vol.9293
    • Chun, S.Y.1    Johnson, C.2    Washburn, J.G.3    Cruz-Correa, M.R.4    Dang, D.T.5    Dang, L.H.6
  • 27
    • 67049159812 scopus 로고    scopus 로고
    • A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation
    • 2-s2.0-67049159812 10.1371/journal.pcbi.1000382 e1000382
    • Hudson N. J., Reverter A., Dalrymple B. P., A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Computational Biology 2009 5 5 2-s2.0-67049159812 10.1371/journal.pcbi.1000382 e1000382
    • (2009) PLoS Computational Biology , vol.5 , Issue.5
    • Hudson, N.J.1    Reverter, A.2    Dalrymple, B.P.3
  • 30
    • 4544326058 scopus 로고    scopus 로고
    • Recent translational research: Microarray expression profiling of breast cancer - Beyond classification and prognostic markers?
    • DOI 10.1186/bcr917
    • Wilson C. A., Dering J., Recent translational research: microarray expression profiling of breast cancer. Beyond classification and prognostic markers? Breast Cancer Research 2004 6 5 192 200 2-s2.0-4544326058 10.1186/bcr917 (Pubitemid 39220373)
    • (2004) Breast Cancer Research , vol.6 , Issue.5 , pp. 192-200
    • Wilson, C.A.1    Dering, J.2
  • 31
    • 0242442571 scopus 로고    scopus 로고
    • The Gene Expression Response of Breast Cancer to Growth Regulators: Patterns and Correlation with Tumor Expression Profiles
    • Cunliffe H. E., Ringnér M., Bilke S., Walker R. L., Cheung J. M., Chen Y., Meltzer P. S., The gene expression response of breast cancer to growth regulators: patterns and correlation with tumor expression profiles. Cancer Research 2003 63 21 7158 7166 2-s2.0-0242442571 (Pubitemid 37413453)
    • (2003) Cancer Research , vol.63 , Issue.21 , pp. 7158-7166
    • Cunliffe, H.E.1    Ringner, M.2    Bilke, S.3    Walker, R.L.4    Cheung, J.M.5    Chen, Y.6    Meltzer, P.S.7
  • 32
    • 1242338758 scopus 로고    scopus 로고
    • Selective Estrogen Receptor Modulators: Discrimination of Agonistic versus Antagonistic Activities by Gene Expression Profiling in Breast Cancer Cells
    • DOI 10.1158/0008-5472.CAN-03-3326
    • Frasor J., Stossi F., Danes J. M., Komm B., Lyttle C. R., Katzenellenbogen B. S., Selective estrogen receptor modulators: discrimination of agonistic versus antagonistic activities by gene expression profiling in breast cancer cells. Cancer Research 2004 64 4 1522 1533 2-s2.0-1242338758 10.1158/0008-5472.CAN-03-3326 (Pubitemid 38235626)
    • (2004) Cancer Research , vol.64 , Issue.4 , pp. 1522-1533
    • Frasor, J.1    Stossi, F.2    Danes, J.M.3    Komm, B.4    Lyttle, C.R.5    Katzenellenbogen, B.S.6
  • 35
    • 84855846735 scopus 로고    scopus 로고
    • Comparing statistical methods for constructing large scale gene networks
    • e29348 10.1371/journal.pone.0029348
    • Allen J. D., Xie Y., Chen M., Girard L., Xiao G., Comparing statistical methods for constructing large scale gene networks. PLoS ONE 2012 7 1 e29348 10.1371/journal.pone.0029348
    • (2012) PLoS ONE , vol.7 , Issue.1
    • Allen, J.D.1    Xie, Y.2    Chen, M.3    Girard, L.4    Xiao, G.5
  • 36
    • 85032751772 scopus 로고    scopus 로고
    • Reverse engineering gene regulatory networks: A survey of statistical models
    • 2-s2.0-61549115055 10.1109/MSP.2008.930647
    • Huang Y., Tienda-Luna I. M., Wang Y., Reverse engineering gene regulatory networks: a survey of statistical models. IEEE Signal Processing Magazine 2009 26 1 76 97 2-s2.0-61549115055 10.1109/MSP.2008.930647
    • (2009) IEEE Signal Processing Magazine , vol.26 , Issue.1 , pp. 76-97
    • Huang, Y.1    Tienda-Luna, I.M.2    Wang, Y.3
  • 37
    • 0014937223 scopus 로고
    • Central dogma of molecular biology
    • 2-s2.0-0014937223 10.1038/227561a0
    • Crick F., Central dogma of molecular biology. Nature 1970 227 5258 561 563 2-s2.0-0014937223 10.1038/227561a0
    • (1970) Nature , vol.227 , Issue.5258 , pp. 561-563
    • Crick, F.1
  • 38
    • 0033744498 scopus 로고    scopus 로고
    • The contribution of molecular markers to the prediction of response in the treatment of breast cancer: A review of the literature on HER-2, p53 and BCL-2
    • 2-s2.0-0033744498 10.1023/A:1008390429428
    • Hamilton A., Piccart M., The contribution of molecular markers to the prediction of response in the treatment of breast cancer: a review of the literature on HER-2, p53 and BCL-2. Annals of Oncology 2000 11 6 647 663 2-s2.0-0033744498 10.1023/A:1008390429428
    • (2000) Annals of Oncology , vol.11 , Issue.6 , pp. 647-663
    • Hamilton, A.1    Piccart, M.2
  • 42
    • 16844376909 scopus 로고    scopus 로고
    • Reverse engineering of regulatory networks in human B cells
    • 2-s2.0-16844376909 10.1038/ng1532
    • Basso K., Margolin A. A., Stolovitzky G., Klein U., Dalla-Favera R., Califano A., Reverse engineering of regulatory networks in human B cells. Nature Genetics 2005 37 4 382 390 2-s2.0-16844376909 10.1038/ng1532
    • (2005) Nature Genetics , vol.37 , Issue.4 , pp. 382-390
    • Basso, K.1    Margolin, A.A.2    Stolovitzky, G.3    Klein, U.4    Dalla-Favera, R.5    Califano, A.6
  • 43
    • 48849090016 scopus 로고    scopus 로고
    • Gene regulatory network reconstruction using conditional mutual information
    • 2-s2.0-48849090016 10.1155/2008/253894 253894
    • Liang K. C., Wang X., Gene regulatory network reconstruction using conditional mutual information. Eurasip Journal on Bioinformatics and Systems Biology 2008 2008 2-s2.0-48849090016 10.1155/2008/253894 253894
    • (2008) Eurasip Journal on Bioinformatics and Systems Biology , vol.2008
    • Liang, K.C.1    Wang, X.2
  • 45
    • 77249109446 scopus 로고    scopus 로고
    • Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
    • ARTICLE 4 2-s2.0-77249109446 10.1186/1748-7188-5-4
    • Hansen M., Everett L., Singh L., Hannenhalli S., Mimosa: mixture model of co-expression to detect modulators of regulatory interaction. Algorithms for Molecular Biology 2010 5 1, article 4 2-s2.0-77249109446 10.1186/1748-7188-5-4
    • (2010) Algorithms for Molecular Biology , vol.5 , Issue.1
    • Hansen, M.1    Everett, L.2    Singh, L.3    Hannenhalli, S.4
  • 46
    • 77957226956 scopus 로고    scopus 로고
    • Discovering modulators of gene expression
    • 2-s2.0-77957226956 10.1093/nar/gkq287 gkq287
    • Babur O., Demir E., Gönen M., Sander C., Dogrusoz U., Discovering modulators of gene expression. Nucleic Acids Research 2010 38 17 5648 5656 2-s2.0-77957226956 10.1093/nar/gkq287 gkq287
    • (2010) Nucleic Acids Research , vol.38 , Issue.17 , pp. 5648-5656
    • Babur, O.1    Demir, E.2    Gönen, M.3    Sander, C.4    Dogrusoz, U.5
  • 47
    • 79958139080 scopus 로고    scopus 로고
    • A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition
    • 2-s2.0-79958139080 10.1371/journal.pone.0020804 e20804
    • Shimamura T., Imoto S., Shimada Y., Hosono Y., Niida A., Nagasaki M., Yamaguchi R., Takahashi T., Miyano S., A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition. PLoS ONE 2011 6 6 2-s2.0-79958139080 10.1371/journal.pone.0020804 e20804
    • (2011) PLoS ONE , vol.6 , Issue.6
    • Shimamura, T.1    Imoto, S.2    Shimada, Y.3    Hosono, Y.4    Niida, A.5    Nagasaki, M.6    Yamaguchi, R.7    Takahashi, T.8    Miyano, S.9
  • 48
    • 84876079151 scopus 로고    scopus 로고
    • A modulator based regulatory network for ERalpha signaling pathway
    • Supplement 6, article S6
    • Wu H. Y., A modulator based regulatory network for ERalpha signaling pathway. BMC Genomics 2012 13 Supplement 6, article S6
    • (2012) BMC Genomics , vol.13
    • Wu, H.Y.1
  • 52
    • 77956846500 scopus 로고    scopus 로고
    • Improving performance of mammalian microRNA target prediction
    • 2-s2.0-77956846500 10.1186/1471-2105-11-476
    • Liu H., Yue D., Chen Y., Gao S. J., Huang Y., Improving performance of mammalian microRNA target prediction. BMC Bioinformatics 2010 11, article 476 2-s2.0-77956846500 10.1186/1471-2105-11-476
    • (2010) BMC Bioinformatics , vol.11
    • Liu, H.1    Yue, D.2    Chen, Y.3    Gao, S.J.4    Huang, Y.5
  • 53
    • 84878800712 scopus 로고    scopus 로고
    • A Bayesian decision fusion approach for microRNA target prediction
    • Dong Y., A Bayesian decision fusion approach for microRNA target prediction. BMC Genomics 2012 13
    • (2012) BMC Genomics , vol.13
    • Dong, Y.1
  • 54
    • 0034795617 scopus 로고    scopus 로고
    • Proceedings of the 24th annual international ACM SIGIR conference on Research and development in information retrieval 2001 New Orleans, La, USA la 10.1145/383952.384007
    • Asm J. A., Montague M., Models for Metasearch. Proceedings of the 24th annual international ACM SIGIR conference on Research and development in information retrieval 2001 New Orleans, La, USA la 276 284 10.1145/383952.384007
    • Models for Metasearch , pp. 276-284
    • Asm, J.A.1    Montague, M.2


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