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Volumn , Issue , 2009, Pages 450-475

A linear programming framework for inferring gene regulatory networks by integrating heterogeneous data

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EID: 84898495884     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4018/978-1-60566-685-3.ch019     Document Type: Chapter
Times cited : (5)

References (37)
  • 1
    • 0036489210 scopus 로고    scopus 로고
    • Chemical genomics: Discovery of disease genes and drugs
    • doi:10.1016/S1359-6446(02)02185-2
    • Alaoui-Ismaili, M. H., Lomedico, P. T., & Jindal, S. (2002). Chemical genomics: discovery of disease genes and drugs. Drug Discovery Today, 7(5), 292-294. doi:10.1016/S1359-6446(02)02185-2
    • (2002) Drug Discovery Today , vol.7 , Issue.5 , pp. 292-294
    • Alaoui-Ismaili, M.H.1    Lomedico, P.T.2    Jindal, S.3
  • 2
    • 33745449162 scopus 로고    scopus 로고
    • Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
    • doi:10.1016/j.jmb.2006.04.029
    • Balaji, S., Babu, M. M., Iyer, L. M., Luscombe, N. M., & Aravind, L. (2006). Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. Journal of Molecular Biology, 360(1), 213-227. doi:10.1016/j.jmb.2006.04.029
    • (2006) Journal of Molecular Biology , vol.360 , Issue.1 , pp. 213-227
    • Balaji, S.1    Babu, M.M.2    Iyer, L.M.3    Luscombe, N.M.4    Aravind, L.5
  • 4
    • 13744251104 scopus 로고    scopus 로고
    • Inferring combinatorial regulation of transcription in silico
    • doi:10.1093/nar/gki167
    • Bluthgen, N., Kielbasa, S. M., & Herzel, H. (2005). Inferring combinatorial regulation of transcription in silico. Nucleic Acids Research, 33(1), 272-279. doi:10.1093/nar/gki167
    • (2005) Nucleic Acids Research , vol.33 , Issue.1 , pp. 272-279
    • Bluthgen, N.1    Kielbasa, S.M.2    Herzel, H.3
  • 5
    • 0032413411 scopus 로고    scopus 로고
    • Predicting gene regulatory elements in silico on a genomic scale
    • Brazma, A., Jonassen, I., Vilo, J., & Ukkonen, E. (1998). Predicting gene regulatory elements in silico on a genomic scale. Genome Research, 8(11), 1202.
    • (1998) Genome Research , vol.8 , Issue.11 , pp. 1202
    • Brazma, A.1    Jonassen, I.2    Vilo, J.3    Ukkonen, E.4
  • 7
    • 0034710924 scopus 로고    scopus 로고
    • Discovering functional relationships between rna expression and chemotherapeutic susceptibility using relevance networks
    • doi:10.1073/pnas.220392197
    • Butte, A. J., Tamayo, P., Slonim, D., Golub, T. R., & Kohane, I. S. (2000). Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proceedings of the National Academy of Sciences of the United States of America, 97(22), 12182-12186. doi:10.1073/pnas.220392197
    • (2000) Proceedings of the National Academy of Sciences of the United States of America , vol.97 , Issue.22 , pp. 12182-12186
    • Butte, A.J.1    Tamayo, P.2    Slonim, D.3    Golub, T.R.4    Kohane, I.S.5
  • 8
    • 33748694308 scopus 로고    scopus 로고
    • Identification of transcription factor cooperativity via stochastic system model
    • doi:10.1093/bio-informatics/btl380
    • Chang, Y.-H., Wang, Y.-C., & Chen, B.-S. (2006). Identification of transcription factor cooperativity via stochastic system model. Bioinformatics (Oxford, England), 22(18), 2276-2282. doi:10.1093/bio-informatics/btl380
    • (2006) Bioinformatics (Oxford, England) , vol.22 , Issue.18 , pp. 2276-2282
    • Chang, Y.-H.1    Wang, Y.-C.2    Chen, B.-S.3
  • 9
    • 0033736476 scopus 로고    scopus 로고
    • Genetic network inference: From co-expression clustering to reverse engineering
    • doi:10.1093/ bioinformatics/16.8.707
    • D'Haeseleer, P., Liang, S., & Somogyi, R. (2000). Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics (Oxford, England), 16(8), 707-726. doi:10.1093/ bioinformatics/16.8.707
    • (2000) Bioinformatics (Oxford, England) , vol.16 , Issue.8 , pp. 707-726
    • D'Haeseleer, P.1    Liang, S.2    Somogyi, R.3
  • 11
    • 33846036710 scopus 로고    scopus 로고
    • The stanford microarray database: Implementation of new analysis tools and open source release of software
    • doi:10.1093/nar/gkl1019
    • Demeter, J., Beauheim, C., Gollub, J., Hernandez-Boussard, T., Jin, H., & Maier, D. (2007). The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Research, 35(Suppl 1), D766-D770. doi:10.1093/nar/gkl1019
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1 , pp. 766-770
    • Demeter, J.1    Beauheim, C.2    Gollub, J.3    Hernandez-Boussard, T.4    Jin, H.5    Maier, D.6
  • 12
    • 0034760495 scopus 로고    scopus 로고
    • Dynamic models of gene expression and classification
    • doi:10.1007/s101420000035
    • Dewey, T. G., & Galas, D. J. (2001). Dynamic models of gene expression and classification. Functional & Integrative Genomics, 1(4), 269-278. doi:10.1007/s101420000035
    • (2001) Functional & Integrative Genomics , vol.1 , Issue.4 , pp. 269-278
    • Dewey, T.G.1    Galas, D.J.2
  • 13
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles
    • doi:10.1371/journal.pbio.0050008
    • Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., & Cottarel, G. (2007). Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology, 5(1), e8. doi:10.1371/journal.pbio.0050008
    • (2007) PLoS Biology , vol.5 , Issue.1 , pp. 8
    • Faith, J.J.1    Hayete, B.2    Thaden, J.T.3    Mogno, I.4    Wierzbowski, J.5    Cottarel, G.6
  • 14
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • doi:10.1126/science.1094068
    • Friedman, N. (2004). Inferring cellular networks using probabilistic graphical models. Science, 303(5659), 799-805. doi:10.1126/science.1094068
    • (2004) Science , vol.303 , Issue.5659 , pp. 799-805
    • Friedman, N.1
  • 15
    • 0038048325 scopus 로고    scopus 로고
    • Inferring genetic networks and identifying compound mode of action via expression profiling
    • doi:10.1126/ science.1081900
    • Gardner, T. S., di Bernardo, D., Lorenz, D., & Collins, J. J. (2003). Inferring genetic networks and identifying compound mode of action via expression profiling. Science, 301(5629), 102-105. doi:10.1126/ science.1081900
    • (2003) Science , vol.301 , Issue.5629 , pp. 102-105
    • Gardner, T.S.1    di Bernardo, D.2    Lorenz, D.3    Collins, J.J.4
  • 16
    • 14844286390 scopus 로고    scopus 로고
    • Reverse-engineering transcription control networks
    • doi:10.1016/j.plrev.2005.01.001
    • Gardner, T. S., & Faith, J. J. (2005). Reverse-engineering transcription control networks. Physics of Life Reviews, 2(1), 65-88. doi:10.1016/j.plrev.2005.01.001
    • (2005) Physics of Life Reviews , vol.2 , Issue.1 , pp. 65-88
    • Gardner, T.S.1    Faith, J.J.2
  • 17
    • 27644508196 scopus 로고    scopus 로고
    • Constructing and analyzing a large-scale gene-to-gene regulatory network-lasso-constrained inference and biological validation
    • TCBB, doi:10.1109/ TCBB.2005.35
    • Gustafsson, M., Hornquist, M., & Lombardi, A. (2005). Constructing and analyzing a large-scale gene-to-gene regulatory network-Lasso-Constrained inference and biological validation. [TCBB]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2(3), 254-261. doi:10.1109/ TCBB.2005.35
    • (2005) IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol.2 , Issue.3 , pp. 254-261
    • Gustafsson, M.1    Hornquist, M.2    Lombardi, A.3
  • 18
    • 4544352942 scopus 로고    scopus 로고
    • Transcriptional regulatory code of a eukaryotic genome
    • doi:10.1038/nature02800
    • Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., & Danford, T. W. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104. doi:10.1038/nature02800
    • (2004) Nature , vol.431 , pp. 99-104
    • Harbison, C.T.1    Gordon, D.B.2    Lee, T.I.3    Rinaldi, N.J.4    Macisaac, K.D.5    Danford, T.W.6
  • 20
    • 0344464762 scopus 로고    scopus 로고
    • Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic bayesian networks
    • doi:10.1093/bioinformatics/btg313
    • Husmeier, D. (2003). Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics (Oxford, England), 19(17), 2271-2282. doi:10.1093/bioinformatics/btg313
    • (2003) Bioinformatics (Oxford, England) , vol.19 , Issue.17 , pp. 2271-2282
    • Husmeier, D.1
  • 22
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: Integrating omics data sets
    • doi:10.1038/nrm1857
    • Joyce, A. R., & Palsson, B. O. (2006). The model organism as a system: integrating Omics data sets. Nature Reviews. Molecular Cell Biology, 7(3), 198-210. doi:10.1038/nrm1857
    • (2006) Nature Reviews. Molecular Cell Biology , vol.7 , Issue.3 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.O.2
  • 23
    • 13544254744 scopus 로고    scopus 로고
    • Identifying combinatorial regulation of transcription factors and binding motifs
    • doi:10.1186/gb-2004-5-8-r56
    • Kato, M., Hata, N., Banerjee, N., Futcher, B., & Zhang, M. Q. (2006). Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology, 5, R56. doi:10.1186/gb-2004-5-8-r56
    • (2006) Genome Biology , vol.5 , pp. 56
    • Kato, M.1    Hata, N.2    Banerjee, N.3    Futcher, B.4    Zhang, M.Q.5
  • 24
    • 19544364324 scopus 로고    scopus 로고
    • Selective integration of multiple biological data for supervised network inference
    • doi:10.1093/bioinformatics/ bti339
    • Kato, T., Tsuda, K., & Asai, K. (2005). Selective integration of multiple biological data for supervised network inference. Bioinformatics (Oxford, England), 21(10), 2488-2495. doi:10.1093/bioinformatics/ bti339
    • (2005) Bioinformatics (Oxford, England) , vol.21 , Issue.10 , pp. 2488-2495
    • Kato, T.1    Tsuda, K.2    Asai, K.3
  • 25
    • 38549130733 scopus 로고    scopus 로고
    • Stitch: Interaction networks of chemicals and proteins
    • Database issue, doi:10.1093/nar/ gkm795
    • Kuhn, M., von Mering, C., Campillos, M., Jensen, L. J., & Bork, P. (2008). STITCH: Interaction networks of chemicals and proteins. Nucleic Acids Research, 36(Database issue), D684. doi:10.1093/nar/ gkm795
    • (2008) Nucleic Acids Research , vol.36 , pp. 684
    • Kuhn, M.1    von Mering, C.2    Campillos, M.3    Jensen, L.J.4    Bork, P.5
  • 26
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in saccharomyces cerevisiae
    • doi:10.1126/ science.1075090
    • Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., & Gerber, G. K. (2002). Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298(5594), 799-804. doi:10.1126/ science.1075090
    • (2002) Science , vol.298 , Issue.5594 , pp. 799-804
    • Lee, T.I.1    Rinaldi, N.J.2    Robert, F.3    Odom, D.T.4    Bar-Joseph, Z.5    Gerber, G.K.6
  • 27
    • 33846108633 scopus 로고    scopus 로고
    • Bindingdb: A web-accessible database of experimentally determined protein-ligand binding affinities
    • SUPPL. doi:10.1093/nar/gkl999
    • Liu, T., Lin, Y., Wen, X., Jorissen, R. N., & Gilson, M. K. (2007). BindingDB: A Web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Research, 35(Suppl 1), D198-D201. doi:10.1093/nar/gkl999
    • (2007) Nucleic Acids Research , vol.35 , Issue.1 , pp. 198-201
    • Liu, T.1    Lin, Y.2    Wen, X.3    Jorissen, R.N.4    Gilson, M.K.5
  • 28
    • 33947305781 scopus 로고    scopus 로고
    • Aracne: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    • SUPPL. S doi:10.1186/1471-2105-7-S1-S7
    • Margolin, A. A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., & Dalla Favera, R. (2006). ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7(Suppl 1), S7. doi:10.1186/1471-2105-7-S1-S7
    • (2006) BMC Bioinformatics , vol.7 , Issue.1 , pp. 7
    • Margolin, A.A.1    Nemenman, I.2    Basso, K.3    Wiggins, C.4    Stolovitzky, G.5    Dalla Favera, R.6
  • 29
    • 14844307159 scopus 로고    scopus 로고
    • Inferring quantitative models of regulatory networks from expression data
    • SUPPL. doi:10.1093/bioin-formatics/bth941
    • Nachman, I., Regev, A., & Friedman, N. (2004). Inferring quantitative models of regulatory networks from expression data. Bioinformatics (Oxford, England), 20(Suppl 1), i248-i256. doi:10.1093/bioin-formatics/bth941
    • (2004) Bioinformatics (Oxford, England) , vol.20 , Issue.1 , pp. 248-256
    • Nachman, I.1    Regev, A.2    Friedman, N.3
  • 30
    • 27544494569 scopus 로고    scopus 로고
    • Estimating gene regulatory networks and protein-protein interactions of saccharomyces cerevisiae from multiple genome-wide data
    • doi:10.1093/bioinformatics/bti1133
    • Nariai, N., Tamada, Y., Imoto, S., & Miyano, S. (2005). Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. Bioinformatics (Oxford, England), 21(Suppl 2), ii206-ii212. doi:10.1093/bioinformatics/bti1133
    • (2005) Bioinformatics (Oxford, England) , vol.21 , Issue.SUPPL. 2 , pp. 206
    • Nariai, N.1    Tamada, Y.2    Imoto, S.3    Miyano, S.4
  • 32
    • 33644873683 scopus 로고    scopus 로고
    • The yeas-tract database: A tool for the analysis of transcription regulatory associations in saccharomyces cerevisiae
    • SUPPL. doi:10.1093/nar/gkj013
    • Teixeira, M. C., Monteiro, P., Jain, P., Tenreiro, S., Fernandes, A. R., & Mira, N. P. (2006). The YEAS-TRACT database: A tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Research, 34(Suppl 1), D446-D451. doi:10.1093/nar/gkj013
    • (2006) Nucleic Acids Research , vol.34 , Issue.1 , pp. 446-451
    • Teixeira, M.C.1    Monteiro, P.2    Jain, P.3    Tenreiro, S.4    Fernandes, A.R.5    Mira, N.P.6
  • 33
    • 36448970861 scopus 로고    scopus 로고
    • Inferring transcriptional regulatory networks from high-throughput data
    • doi:10.1093/bioin-formatics/btm465
    • Wang, R. S., Wang, Y., Zhang, X. S., & Chen, L. (2007). Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics (Oxford, England), 23(22), 3056-3064. doi:10.1093/bioin-formatics/btm465
    • (2007) Bioinformatics (Oxford, England) , vol.23 , Issue.22 , pp. 3056-3064
    • Wang, R.S.1    Wang, Y.2    Zhang, X.S.3    Chen, L.4
  • 35
    • 33750016109 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from multiple microarray datasets
    • doi:10.1093/bioinformat-ics/btl396
    • Wang, Y., Joshi, T., Zhang, X. S., Xu, D., & Chen, L. (2006). Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (Oxford, England), 22(19), 2413. doi:10.1093/bioinformat-ics/btl396
    • (2006) Bioinformatics (Oxford, England) , vol.22 , Issue.19 , pp. 2413
    • Wang, Y.1    Joshi, T.2    Zhang, X.S.3    Xu, D.4    Chen, L.5
  • 36
    • 38549151817 scopus 로고    scopus 로고
    • Drugbank: A knowledgebase for drugs, drug actions, and drug targets
    • doi:10.1093/nar/gkm958
    • Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., & Tzur, D. (2007). DrugBank: A knowledgebase for drugs, drug actions, and drug targets. Nucleic Acids Research, 36, D901-D906. doi:10.1093/nar/gkm958
    • (2007) Nucleic Acids Research , vol.36 , pp. 901-906
    • Wishart, D.S.1    Knox, C.2    Guo, A.C.3    Cheng, D.4    Shrivastava, S.5    Tzur, D.6


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