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Volumn , Issue , 2009, Pages 476-496

Integrating various data sources for improved quality in reverse engineering of gene regulatory networks

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EID: 78649663202     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4018/978-1-60566-685-3.ch020     Document Type: Chapter
Times cited : (4)

References (44)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • et al, Annotations retrieved in December 2007, from
    • Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., et al. (2000). Gene ontology: Tool for the unification of biology. Naure Genetics, 25, 25-29. Annotations retrieved in December 2007, from http://www.yeastgenome.org/
    • (2000) Naure Genetics , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5    Cherry, J.M.6
  • 2
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • doi:10.1038/nrg1272
    • Barabasi, A. L., & Oltvai, Z. N. (2004). Network biology: Understanding the cell's functional organization. Nature Reviews. Genetics, 5, 101-113. doi:10.1038/nrg1272
    • (2004) Nature Reviews. Genetics , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 3
    • 33747813561 scopus 로고    scopus 로고
    • The inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    • doi:10.1186/gb-2006-7-5-r36
    • Bonneau, R., Reiss, D. J., Shannon, P., Hood, L., Baliga, N. S., & Thorsson, V. (2006). The inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biology, 7(5), R36. doi:10.1186/gb-2006-7-5-r36
    • (2006) Genome Biology , vol.7 , Issue.5 , pp. 36
    • Bonneau, R.1    Reiss, D.J.2    Shannon, P.3    Hood, L.4    Baliga, N.S.5    Thorsson, V.6
  • 4
    • 0036843965 scopus 로고    scopus 로고
    • Gene networks: How to put the function in genomics
    • doi:10.1016/S0167-7799(02)02053-X
    • Brazhnik, P., de la Fuente, A., & Mendes, P. (2002). Gene networks: How to put the function in genomics. Trends in Biotechnology, 20, 467-472. doi:10.1016/S0167-7799(02)02053-X
    • (2002) Trends in Biotechnology , vol.20 , pp. 467-472
    • Brazhnik, P.1    de la Fuente, A.2    Mendes, P.3
  • 5
    • 0032112293 scopus 로고    scopus 로고
    • A genomewide transcriptional analysis of the mitotic cell cycle
    • doi:10.1016/ S1097-2765(00)80114-8
    • Cho, R. J., Campbell, M. J., Winzeler, E. A., Steinmetz, L., Conway, A., & Wodicka, L. (1998). A genomewide transcriptional analysis of the mitotic cell cycle. Molecular Cell, 2, 65-73. doi:10.1016/ S1097-2765(00)80114-8
    • (1998) Molecular Cell , vol.2 , pp. 65-73
    • Cho, R.J.1    Campbell, M.J.2    Winzeler, E.A.3    Steinmetz, L.4    Conway, A.5    Wodicka, L.6
  • 6
    • 0032612220 scopus 로고    scopus 로고
    • Linear modeling of mrna expression levels during cns development and injury
    • In R. B. Altman, A. K. Dunker, L. Hunter, T. E. Klein & K. Lauderdaule (Eds.), Singapore: World Scientific Publishing Co
    • D'haeseleer, P., Wen, X., Fuhrman, S., & Somogyi, R. (1999). Linear modeling of mRNA expression levels during CNS development and injury. In R. B. Altman, A. K. Dunker, L. Hunter, T. E. Klein & K. Lauderdaule (Eds.), Pacific Symposium on Biocomputing, 4, 41-52. Singapore: World Scientific Publishing Co.
    • (1999) Pacific Symposium on Biocomputing , vol.4 , pp. 41-52
    • D'haeseleer, P.1    Wen, X.2    Fuhrman, S.3    Somogyi, R.4
  • 8
    • 84898496079 scopus 로고    scopus 로고
    • DREAM. Dialogue on Reverse-Engineering Assessment and Methods, Retrieved in January 2009, from
    • DREAM. Dialogue on Reverse-Engineering Assessment and Methods. (2007). Retrieved in January 2009, from http://wiki.c2b2.columbia.edu/dream/index.php/The_DREAM_Project
    • (2007)
  • 9
    • 84898510545 scopus 로고    scopus 로고
    • DREAM. Dialogue on Reverse-Engineering Assessment and Methods, Retrieved in January 2009, from
    • DREAM. Dialogue on Reverse-Engineering Assessment and Methods. (2008). Descriptions of the challenges. Retrieved in January 2009, from http://wiki.c2b2.columbia.edu/dream/index.php/The_DREAM3_Challenges
    • (2008) Descriptions of the Challenges
  • 11
    • 0036100833 scopus 로고    scopus 로고
    • Analysis techniques for microarray time-series data
    • doi:10.1089/10665270252935485
    • Filkov, V., Skiena, S., & Zhi, J. (2002). Analysis techniques for microarray time-series data. Journal of Computational Biology, 9, 317-330. doi:10.1089/10665270252935485
    • (2002) Journal of Computational Biology , vol.9 , pp. 317-330
    • Filkov, V.1    Skiena, S.2    Zhi, J.3
  • 12
    • 33750482575 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae s288c genome annotation: A working hypothesis
    • from, Retrieved in December 2007. doi:10.1002/yea.1400
    • Fisk, D. G., Ball, C. A., Dolinski, K., Engel, S. R., Hong, E. L., & Issel-Tarver, L. (2006). Saccharomyces cerevisiae S288C genome annotation: A working hypothesis. [from http://www.yeastgenome.org/]. Yeast (Chichester, England), 23(12), 857-865. Retrieved in December 2007. doi:10.1002/yea.1400
    • (2006) Yeast (Chichester, England) , vol.23 , Issue.12 , pp. 857-865
    • Fisk, D.G.1    Ball, C.A.2    Dolinski, K.3    Engel, S.R.4    Hong, E.L.5    Issel-Tarver, L.6
  • 15
    • 70149116009 scopus 로고    scopus 로고
    • Retrieved in December 2007, from, CPLEX version 10 retrieved from, commercial software
    • Giorgetti, N. (2005). Matlab MEX interface for the CPLEX callable library. Retrieved in December 2007, from http://www.dii.unisi.it/~hybrid/tools/mex/downloads.html CPLEX version 10 retrieved from http://www.ilog.com/ (commercial software)
    • (2005) Matlab MEX Interface for the CPLEX Callable Library
    • Giorgetti, N.1
  • 17
    • 27644508196 scopus 로고    scopus 로고
    • Constructing and analyzing a large-scale gene-to-gene regulatory network-lasso-constrained inference and biological validation
    • doi:10.1109/TCBB.2005.35
    • Gustafsson, M., Hörnquist, M., & Lombardi, A. (2005). Constructing and analyzing a large-scale gene-to-gene regulatory network-lasso-constrained inference and biological validation. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2, 254-261. doi:10.1109/TCBB.2005.35
    • (2005) IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol.2 , pp. 254-261
    • Gustafsson, M.1    Hörnquist, M.2    Lombardi, A.3
  • 18
    • 84898496876 scopus 로고    scopus 로고
    • Gene expression by the elastic net
    • In M. Kellis, A. Califano & G. Stolovitzky (Eds.), Boston, MA
    • Gustafssson, M., & Hörnquist, M. (2008). Gene expression by the elastic net. In M. Kellis, A. Califano & G. Stolovitzky (Eds.), DREAM3, RECOMB satellite proceedings (p. 48 and p. 133). Boston, MA.
    • (2008) DREAM3, RECOMB Satellite Proceedings , pp. 48
    • Gustafssson, M.1    Hörnquist, M.2
  • 22
    • 0035805255 scopus 로고    scopus 로고
    • Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
    • doi:10.1126/science.292.5518.929
    • Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., & Eng, J. K. (2001). Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 292(5518), 929-934. doi:10.1126/science.292.5518.929
    • (2001) Science , vol.292 , Issue.5518 , pp. 929-934
    • Ideker, T.1    Thorsson, V.2    Ranish, J.A.3    Christmas, R.4    Buhler, J.5    Eng, J.K.6
  • 24
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • doi:10.1038/nature02782
    • Luscombe, N. M., Babu, M. M., Yu, H., Snyder, M., Teichmann, S. A., & Gerstein, M. (2004). Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431, 308-312. doi:10.1038/nature02782
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5    Gerstein, M.6
  • 25
    • 44949214875 scopus 로고    scopus 로고
    • Proximity of intracellular regulatory networks to monotone systems
    • doi:10.1049/iet-syb:20070036
    • Ma'ayan, A., Lipshtat, A., Iyengar, R., & Sontag, E. D. (2008). Proximity of intracellular regulatory networks to monotone systems. IET Systems Biology, 2, 103-112. doi:10.1049/iet-syb:20070036
    • (2008) IET Systems Biology , vol.2 , pp. 103-112
    • Ma'ayan, A.1    Lipshtat, A.2    Iyengar, R.3    Sontag, E.D.4
  • 26
    • 33645743420 scopus 로고    scopus 로고
    • The more the merrier: Comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast
    • doi:10.1002/yea.1351
    • Marguerat, S., Jensen, T. S., de Lichtenberg, U., Wilhelm, B. T., Jensen, L. J., & Bähler, J. (2006). The more the merrier: Comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast. Yeast (Chichester, England), 23, 261-277. doi:10.1002/yea.1351
    • (2006) Yeast (Chichester, England) , vol.23 , pp. 261-277
    • Marguerat, S.1    Jensen, T.S.2    de Lichtenberg, U.3    Wilhelm, B.T.4    Jensen, L.J.5    Bähler, J.6
  • 27
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • doi:10.1126/science.298.5594.824
    • Milo, R., Shen-Orr, S., Itzkovitz, N., Kashtan, D., Chklovskii, D., & Alon, U. (2002). Network motifs: Simple building blocks of complex networks. Science, 298, 824-827. doi:10.1126/science.298.5594.824
    • (2002) Science , vol.298 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, N.3    Kashtan, D.4    Chklovskii, D.5    Alon, U.6
  • 28
    • 0004211673 scopus 로고    scopus 로고
    • Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
    • Ptashne, M., & Gann, A. (2002). Genes and signals. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
    • (2002) Genes and Signals
    • Ptashne, M.1    Gann, A.2
  • 29
    • 84898526214 scopus 로고    scopus 로고
    • PubMed, Retrieved in December 2007, from
    • PubMed. (2007). Retrieved in December 2007, from http://www.ncbi.nlm.nih.gov/sites/entrez/
    • (2007)
  • 31
    • 22844446947 scopus 로고    scopus 로고
    • An integrative genomics approach to infer causal associations between gene expression and disease
    • doi:10.1038/ng1589
    • Schadt, E. E., Lamb, J., Yang, X., Zhu, J., Edwards, S., & Guhathakurta, D. (2005). An integrative genomics approach to infer causal associations between gene expression and disease. Nature Genetics, 37, 710-717. doi:10.1038/ng1589
    • (2005) Nature Genetics , vol.37 , pp. 710-717
    • Schadt, E.E.1    Lamb, J.2    Yang, X.3    Zhu, J.4    Edwards, S.5    Guhathakurta, D.6
  • 32
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
    • doi:10.1038/ng1165
    • Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D., & Friedman, N. (2003). Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics, 34(2), 166-176. doi:10.1038/ng1165
    • (2003) Nature Genetics , vol.34 , Issue.2 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 33
    • 0742321914 scopus 로고    scopus 로고
    • Regression approaches for microarray data analysis
    • doi:10.1089/106652703322756177
    • Segal, M. R. (2003). Regression approaches for microarray data analysis. Journal of Computational Biology, 10(6), 961-980. doi:10.1089/106652703322756177
    • (2003) Journal of Computational Biology , vol.10 , Issue.6 , pp. 961-980
    • Segal, M.R.1
  • 34
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization
    • Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., & Eisen, M. B. (1998). Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell, 9, 3273-3297.
    • (1998) Molecular Biology of the Cell , vol.9 , pp. 3273-3297
    • Spellman, P.T.1    Sherlock, G.2    Zhang, M.Q.3    Iyer, V.R.4    Anders, K.5    Eisen, M.B.6
  • 35
    • 33644873683 scopus 로고    scopus 로고
    • The yeastract database: A tool for the analysis of transcription regulatory associations
    • et al., in, Oxford University Press. Retrieved in December 2007, from
    • Teixeira, M. C., Monteiro, P., Jain, P., Tenreiro, S., Fernandes, A. R., Mira, N. P., et al. (2006). The YEASTRACT database: A tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae, Nucleic Acids Research, 34, D446-D451. Oxford University Press. Retrieved in December 2007, from http://www.yeastract.com
    • (2006) Saccharomyces Cerevisiae, Nucleic Acids Research , vol.34 , pp. 446
    • Teixeira, M.C.1    Monteiro, P.2    Jain, P.3    Tenreiro, S.4    Fernandes, A.R.5    Mira, N.P.6
  • 39
    • 0037399803 scopus 로고    scopus 로고
    • Multicriterion optimization for genetic network modelling
    • doi:10.1016/S0165-1684(02)00473-5
    • van Someren, E. P., Wessels, E., Backer, L. F. A., & Reinders, M. J. T. (2003). Multicriterion optimization for genetic network modelling. Signal Processing, 83, 763-775. doi:10.1016/S0165-1684(02)00473-5
    • (2003) Signal Processing , vol.83 , pp. 763-775
    • van Someren, E.P.1    Wessels, E.2    Backer, L.F.A.3    Reinders, M.J.T.4
  • 41
    • 33750016109 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from multiple microarray datasets
    • doi:10.1093/bioinfor-matics/btl396
    • Wang, Y., Trupti, J., Zhang, X., Xu, D., & Chen, L. (2006). Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (Oxford, England), 22, 2413-2420. doi:10.1093/bioinfor-matics/btl396
    • (2006) Bioinformatics (Oxford, England) , vol.22 , pp. 2413-2420
    • Wang, Y.1    Trupti, J.2    Zhang, X.3    Xu, D.4    Chen, L.5
  • 42
    • 0033971642 scopus 로고    scopus 로고
    • Dip: The database of interacting proteins
    • from, Retrieved in December 2007. doi:10.1093/nar/28.1.289
    • Xenarios, I., Rice, D. W., Salwinski, L., Baron, M. K., Marcotte, E. M., & Eisenberg, D. (2000). DIP: The database of interacting proteins. [from http://dip.doe-mbi.ucla.edu/]. Nucleic Acids Research, 28, 289-291. Retrieved in December 2007. doi:10.1093/nar/28.1.289
    • (2000) Nucleic Acids Research , vol.28 , pp. 289-291
    • Xenarios, I.1    Rice, D.W.2    Salwinski, L.3    Baron, M.K.4    Marcotte, E.M.5    Eisenberg, D.6
  • 44
    • 16244401458 scopus 로고    scopus 로고
    • Regularization and variable selection via the elastic net
    • doi:10.1111/j.1467-9868.2005.00503.x
    • Zou, H., & Hastie, T. (2005). Regularization and variable selection via the elastic net. Journal of the Royal Statistical Society. Series B. Methodological, 67(2), 301-320. doi:10.1111/j.1467-9868.2005.00503.x
    • (2005) Journal of the Royal Statistical Society. Series B. Methodological , vol.67 , Issue.2 , pp. 301-320
    • Zou, H.1    Hastie, T.2


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